6KSV | pdb_00006ksv

Crystal structure of SurE with D-Leu

PDB DOI: https://doi.org/10.2210/pdb6KSV/pdb

Classification: HYDROLASE
Organism(s): Streptomyces albidoflavus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-08-26 Released: 2020-06-24
Deposition Author(s): Zhai, R., Mori, T., Abe, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Heterochiral coupling in non-ribosomal peptide macrolactamization

Matsuda, K., Zhai, R., Mori, T., Kobayashi, M., Sano, A., Abe, I., Wakimoto, T.

(2020) Nat Catal

DOI: https://doi.org/10.1038/s41929-020-0456-7

Macromolecule Content

Total Structure Weight: 100.4 kDa
Atom Count: 6,489
Modelled Residue Count: 853
Deposited Residue Count: 942
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase	A, B	471	Streptomyces albidoflavus	Mutation(s): 0
UniProt
Find proteins for A0A679G4U8 (Streptomyces albidoflavus) Explore A0A679G4U8 Go to UniProtKB: A0A679G4U8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A679G4U8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E7L (Subject of Investigation/LOI) Query on E7L Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	S-(2-acetamidoethyl) (2R)-2-azanyl-4-methyl-pentanethioate C₁₀ H₂₀ N₂ O₂ S FGUKBCKKFXHYHQ-SECBINFHSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DLE (Subject of Investigation/LOI) Query on DLE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	D-LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-RXMQYKEDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
YT3 Query on YT3 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	G [auth A], H [auth A], L [auth B]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.37	α = 90
b = 152.06	β = 113.08
c = 64.54	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Zhai, R.

Mori, T.

Abe, I.

Revision History (Full details and data files)

Version 1.0: 2020-06-24
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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Crystal structure of SurE with D-Leu

Heterochiral coupling in non-ribosomal peptide macrolactamization

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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