7CX7 | pdb_00007cx7

Crystal structure of Arabinose isomerase from hybrid AI8

PDB DOI: https://doi.org/10.2210/pdb7CX7/pdb

Classification: ISOMERASE
Organism(s): Geobacillus kaustophilus HTA426, Alicyclobacillus sp. TP7, Alicyclobacillus acidocaldarius subsp. acidocaldarius
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-09-01 Released: 2021-09-01
Deposition Author(s): Hoang, N.K.Q., Dhanasingh, I., Cao, T.P., Sung, J.Y., Shin, S.M., Lee, D.W., Lee, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.268 (Depositor), 0.264 (DCC)
R-Value Work:
0.192 (Depositor), 0.193 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7CX7

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

Literature

Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) wt

Hoang, N.K.Q., Dhanasingh, I., Cao, T.P., Sung, J.Y., Shin, S.M., Lee, D.W., Lee, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 337.34 kDa
Atom Count: 23,927
Modeled Residue Count: 2,964
Deposited Residue Count: 2,982
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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, Alicyclobacillus sp. TP7, Alicyclobacillus acidocaldarius subsp. acidocaldarius	Mutation(s): 0 Gene Names: araA, GK1904 EC: 5.3.1.4
UniProt
Find proteins for K0IGW6 (Alicyclobacillus sp. TP7) Explore K0IGW6 Go to UniProtKB: K0IGW6
Find proteins for Q5KYP7 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KYP7 Go to UniProtKB: Q5KYP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q5KYP7 K0IGW6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F]	G [auth A] H [auth A] K [auth B] M [auth C] N [auth C] G [auth A], H [auth A], K [auth B], M [auth C], N [auth C], S [auth E], T [auth E], W [auth F], X [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain W [auth F] Focus chain X [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain Y [auth F] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain J [auth A]	I [auth A] J [auth A] L [auth B] P [auth C] Q [auth C] I [auth A], J [auth A], L [auth B], P [auth C], Q [auth C], R [auth D], U [auth E], V [auth E], Y [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.268 (Depositor), 0.264 (DCC)
R-Value Work: 0.192 (Depositor), 0.193 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.591	α = 90
b = 81.907	β = 117.9
c = 192.001	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-01
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, 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.