4R1Q | pdb_00004r1q

Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol

PDB DOI: https://doi.org/10.2210/pdb4R1Q/pdb

Classification: ISOMERASE
Organism(s): Geobacillus kaustophilus HTA426
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-07 Released: 2015-08-12
Deposition Author(s): Choi, J.M., Lee, Y.J., Lee, D.W., Lee, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.154 (Depositor), 0.150 (DCC)
R-Value Observed:
0.156 (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

Crystal Structure of Thermophilic L-Arabinose Isomerase with L-Arabitol from Geobacillus kaustophilus

Choi, J.M., Lee, Y.J., Lee, D.W., Lee, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 339.07 kDa
Atom Count: 25,396
Modeled Residue Count: 2,972
Deposited Residue Count: 2,982
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-arabinose isomerase	A, B, C, D, E A, B, C, D, E, F	497	Geobacillus kaustophilus HTA426	Mutation(s): 0 Gene Names: araA, GK1904 EC: 5.3.1.4
UniProt
Find proteins for Q5KYP7 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KYP7 Go to UniProtKB: Q5KYP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5KYP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SST Query on SST Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth E]	G [auth A] H [auth A] J [auth B] L [auth C] M [auth C] G [auth A], H [auth A], J [auth B], L [auth C], M [auth C], P [auth E]	L-arabinitol C₅ H₁₂ O₅ HEBKCHPVOIAQTA-IMJSIDKUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth E]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F]	I [auth A] K [auth B] N [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], N [auth C], O [auth D], Q [auth E], R [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.154 (Depositor), 0.150 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.514	α = 90
b = 146.263	β = 90
c = 215.677	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2015-10-21
Changes: Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol

Crystal Structure of Thermophilic L-Arabinose Isomerase with L-Arabitol from Geobacillus kaustophilus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations