5MBS | pdb_00005mbs

Crystal structure of Bacillus subtilis EngA in space group P21

PDB DOI: https://doi.org/10.2210/pdb5MBS/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-08 Released: 2017-12-20
Deposition Author(s): da Silveira Tome, C., Foucher, A.E., Jault, J.M., Housset, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.373 (Depositor), 0.365 (DCC)
R-Value Work:
0.220 (Depositor), 0.223 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Bacillus subtilis EngA in space group P21

da Silveira Tome, C., Foucher, A.E., Jault, J.M., Housset, D.

To be published.

Macromolecule Content

Total Structure Weight: 49.37 kDa
Atom Count: 3,222
Modeled Residue Count: 403
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase Der	A	436	Bacillus subtilis	Mutation(s): 0 Gene Names: der, B4122_2158, B4417_1159
UniProt
Find proteins for P50743 (Bacillus subtilis (strain 168)) Explore P50743 Go to UniProtKB: P50743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50743
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.373 (Depositor), 0.365 (DCC)
R-Value Work: 0.220 (Depositor), 0.223 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.92	α = 90
b = 64.15	β = 96.39
c = 62.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

da Silveira Tome, C.

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.