3S47 | pdb_00003s47

Crystal structure of enolase superfamily member from Clostridium beijerincki complexed with Mg

PDB DOI: https://doi.org/10.2210/pdb3S47/pdb

Classification: ISOMERASE
Organism(s): Clostridium beijerinckii NCIMB 8052
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-18 Released: 2012-05-23
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.285 (Depositor), 0.275 (DCC)
R-Value Work:
0.243 (Depositor), 0.235 (DCC)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3S47

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

Literature

Crystal structure of enolase superfamily member from Clostridium beijerincki complexed with Mg

Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 91.07 kDa
Atom Count: 6,509
Modeled Residue Count: 772
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B	401	Clostridium beijerinckii NCIMB 8052	Mutation(s): 0 Gene Names: Cbei_4837
UniProt
Find proteins for A6M2W4 (Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)) Explore A6M2W4 Go to UniProtKB: A6M2W4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6M2W4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.285 (Depositor), 0.275 (DCC)
R-Value Work: 0.243 (Depositor), 0.235 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.259	α = 90
b = 111.259	β = 90
c = 139.803	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.