3OUZ | pdb_00003ouz

Crystal Structure of Biotin Carboxylase-ADP complex from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb3OUZ/pdb

Classification: LIGASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-15 Released: 2010-10-13
Deposition Author(s): Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.181 (Depositor), 0.178 (DCC)
R-Value Work:
0.150 (Depositor), 0.147 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Biotin Carboxylase-ADP complex from Campylobacter jejuni

Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 103.31 kDa
Atom Count: 8,979
Modelled Residue Count: 888
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin carboxylase	A, B	446	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 Gene Names: accC, Cj1290c EC: 6.3.4.14 (PDB Primary Data), 6.4.1.2 (PDB Primary Data)
UniProt
Find proteins for Q0P8W7 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P8W7 Go to UniProtKB: Q0P8W7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0P8W7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain U [auth B] mmCIF format, chain H [auth A] mmCIF format, chain U [auth B]	H [auth A], U [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain U [auth B]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
SRT Query on SRT Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], K [auth A], N [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], X [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth B] Focus chain Z [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain T [auth B] SDF format, chain J [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth B] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth B] mmCIF format, chain J [auth A]	AA [auth B], J [auth A], M [auth A], O [auth B], T [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain J [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain T [auth B] Interactions & Density Focus chain AA [auth B] Focus chain J [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain T [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain V [auth B]	I [auth A], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain V [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.181 (Depositor), 0.178 (DCC)
R-Value Work: 0.150 (Depositor), 0.147 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33ouz

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.855	α = 90
b = 100.674	β = 90
c = 147.702	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELX	model building
RESOLVE	model building
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
RESOLVE	phasing
BUCCANEER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 1.3: 2024-11-20
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary