7CH3 | pdb_00007ch3

Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)

PDB DOI: https://doi.org/10.2210/pdb7CH3/pdb

Classification: ISOMERASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-07-04 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: 3.61 Å
R-Value Free:
0.280 (Depositor), 0.279 (DCC)
R-Value Work:
0.232 (Depositor), 0.231 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7CH3

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

Literature

Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)

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: 679.73 kDa
Atom Count: 47,435
Modeled Residue Count: 5,914
Deposited Residue Count: 5,952
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, G, H, I, J, K, L	496	Thermotoga maritima MSB8	Mutation(s): 3 Gene Names: araA, TM_0276 EC: 5.3.1.4
UniProt
Find proteins for Q9WYB3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYB3 Go to UniProtKB: Q9WYB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 AA [auth J] SDF format, chain DA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain W [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] SDF format, chain CA [auth L] SDF format, chain BA [auth K] MOL2 format, chain AA [auth J] MOL2 format, chain DA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain W [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] MOL2 format, chain CA [auth L] MOL2 format, chain BA [auth K] mmCIF format, chain AA [auth J] mmCIF format, chain DA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain W [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J] mmCIF format, chain CA [auth L] mmCIF format, chain BA [auth K]	AA [auth J] BA [auth K] CA [auth L] DA [auth L] M [auth A] AA [auth J], BA [auth K], CA [auth L], DA [auth L], M [auth A], N [auth A], O [auth B], P [auth C], Q [auth C], R [auth D], S [auth E], T [auth E], U [auth F], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.61 Å
R-Value Free: 0.280 (Depositor), 0.279 (DCC)
R-Value Work: 0.232 (Depositor), 0.231 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.424	α = 81.08
b = 113.913	β = 81.15
c = 160.833	γ = 88.89

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-10-20

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.