3RE3 | pdb_00003re3

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from Francisella tularensis

PDB DOI: https://doi.org/10.2210/pdb3RE3/pdb

Classification: LYASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-02 Released: 2011-04-27
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.227 (Depositor), 0.217 (DCC)
R-Value Work:
0.173 (Depositor), 0.167 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from Francisella tularensis

Kim, Y., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 73.61 kDa
Atom Count: 4,772
Modelled Residue Count: 583
Deposited Residue Count: 648
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A, B, C, D	162	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 Gene Names: FTT_1128, ispF EC: 4.6.1.12
UniProt
Find proteins for Q5NFU1 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NFU1 Go to UniProtKB: Q5NFU1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NFU1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth C]	L [auth C], N [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain L [auth C] Focus chain N [auth C] Interactions & Density Focus chain L [auth C] Focus chain N [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	H [auth A], K [auth C], O [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth C] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain P [auth D]	G [auth A], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	F [auth A], J [auth B], M [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.227 (Depositor), 0.217 (DCC)
R-Value Work: 0.173 (Depositor), 0.167 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33re3

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.116	α = 90
b = 96.116	β = 90
c = 155.308	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary