7CHL | pdb_00007chl

Crystal structure of hybrid Arabinose isomerase AI-10

PDB DOI: https://doi.org/10.2210/pdb7CHL/pdb

Classification: ISOMERASE
Organism(s): Alicyclobacillus sp. TP7, Geobacillus kaustophilus HTA426, Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-07-06 Released: 2021-10-20
Deposition Author(s): Cao, T.P., Dhanasingh, I., Sung, J.Y., Shin, S.M., Lee, D.W., Lee, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.264 (Depositor), 0.263 (DCC)
R-Value Work:
0.208 (Depositor), 0.208 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hybrid Arabinose isomerase AI-10

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

To be published.

Macromolecule Content

Total Structure Weight: 671.96 kDa
Atom Count: 47,178
Modeled Residue Count: 5,969
Deposited Residue Count: 5,976
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hybrid Arabinose isomerase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	498	Alicyclobacillus sp. TP7, Geobacillus kaustophilus HTA426, Escherichia coli K-12	Mutation(s): 0 Gene Names: araA, GK1904, b0062, JW0061 EC: 5.3.1.4
UniProt
Find proteins for K0IGW6 (Alicyclobacillus sp. TP7) Explore K0IGW6 Go to UniProtKB: K0IGW6
Find proteins for P08202 (Escherichia coli (strain K12)) Explore P08202 Go to UniProtKB: P08202
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 P08202
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain IA [auth L] SDF format, chain GA [auth K] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain AA [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain JA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain DA [auth I] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.264 (Depositor), 0.263 (DCC)
R-Value Work: 0.208 (Depositor), 0.208 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.086	α = 90
b = 164.297	β = 119.92
c = 151.973	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-10-20
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.