4Z4J | pdb_00004z4j

Crystal Structure of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus DSM 8903

PDB DOI: https://doi.org/10.2210/pdb4Z4J/pdb

Classification: ISOMERASE
Organism(s): Caldicellulosiruptor saccharolyticus DSM 8903
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-04-02 Released: 2016-04-13
Deposition Author(s): Shen, Q.Y., Zhang, Y.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.159 (Depositor), 0.162 (DCC)
R-Value Observed:
0.160 (Depositor)

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

Literature

Crystal Structure of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus DSM 8903

Shen, Q.Y., Zhang, Y.Z.

To be published.

Macromolecule Content

Total Structure Weight: 48.13 kDa
Atom Count: 3,700
Modeled Residue Count: 392
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose 2-epimerase	A	402	Caldicellulosiruptor saccharolyticus DSM 8903	Mutation(s): 0 Gene Names: Csac_0294 EC: 5.1.3.11
UniProt
Find proteins for A4XGA6 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XGA6 Go to UniProtKB: A4XGA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XGA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.159 (Depositor), 0.162 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.687	α = 90
b = 75.773	β = 90
c = 91.171	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2024-03-06
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.