3WIR

Crystal structure of kojibiose phosphorylase complexed with glucose

PDB DOI: https://doi.org/10.2210/pdb3WIR/pdb

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

Deposited: 2013-09-24 Released: 2014-02-05
Deposition Author(s): Okada, S., Yamamoto, T., Watanabe, H., Nishimoto, T., Chaen, H., Fukuda, S., Wakagi, T., Fushinobu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.251
R-Value Work: 0.191
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 357.58 kDa
Atom Count: 26,306
Modelled Residue Count: 3,024
Deposited Residue Count: 3,056
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kojibiose phosphorylase	A, B, C, D	764	Caldicellulosiruptor saccharolyticus DSM 8903	Mutation(s): 0 Gene Names: Csac_0444 EC: 2.4.1.230
UniProt
Find proteins for A4XGP2 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XGP2 Go to UniProtKB: A4XGP2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4XGP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D]	E [auth A] F [auth A] J [auth B] K [auth B] O [auth C] E [auth A], F [auth A], J [auth B], K [auth B], O [auth C], P [auth C], U [auth D], V [auth D]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	AA [auth D] I [auth A] M [auth B] N [auth B] S [auth C] AA [auth D], I [auth A], M [auth B], N [auth B], S [auth C], T [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	G [auth A] H [auth A] L [auth B] Q [auth C] R [auth C] G [auth A], H [auth A], L [auth B], Q [auth C], R [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.251
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.581	α = 68.83
b = 104.464	β = 86.02
c = 124.164	γ = 90.06

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-05
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary