1VPX | pdb_00001vpx

Crystal structure of Transaldolase (EC 2.2.1.2) (TM0295) from Thermotoga maritima at 2.40 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VPX/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-11-23 Released: 2004-12-07
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.247 (Depositor), 0.251 (DCC)
R-Value Work:
0.196 (Depositor), 0.204 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1VPX

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Transaldolase (EC 2.2.1.2) (TM0295) from Thermotoga maritima at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 516.09 kDa
Atom Count: 31,916
Modeled Residue Count: 4,176
Deposited Residue Count: 4,600
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Transaldolase (EC 2.2.1.2))	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	230	Thermotoga maritima	Mutation(s): 0 Gene Names: TM0295 EC: 2.2.1.2
UniProt
Find proteins for Q9WYD1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYD1 Go to UniProtKB: Q9WYD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth O] MOL2 format, chain IA [auth O] mmCIF format, chain IA [auth O]	IA [auth O]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth O] Interactions & Density Focus chain IA [auth O]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth E] SDF format, chain X [auth D] SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth A] SDF format, chain PA [auth T] SDF format, chain OA [auth S] SDF format, chain NA [auth R] SDF format, chain MA [auth Q] SDF format, chain LA [auth P] SDF format, chain KA [auth P] SDF format, chain JA [auth O] SDF format, chain HA [auth N] SDF format, chain GA [auth M] SDF format, chain FA [auth L] SDF format, chain EA [auth K] SDF format, chain DA [auth J] SDF format, chain CA [auth I] SDF format, chain BA [auth H] SDF format, chain AA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth A] MOL2 format, chain PA [auth T] MOL2 format, chain OA [auth S] MOL2 format, chain NA [auth R] MOL2 format, chain MA [auth Q] MOL2 format, chain LA [auth P] MOL2 format, chain KA [auth P] MOL2 format, chain JA [auth O] MOL2 format, chain HA [auth N] MOL2 format, chain GA [auth M] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth A] mmCIF format, chain PA [auth T] mmCIF format, chain OA [auth S] mmCIF format, chain NA [auth R] mmCIF format, chain MA [auth Q] mmCIF format, chain LA [auth P] mmCIF format, chain KA [auth P] mmCIF format, chain JA [auth O] mmCIF format, chain HA [auth N] mmCIF format, chain GA [auth M] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth H] CA [auth I] DA [auth J] EA [auth K] AA [auth G], BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], JA [auth O], KA [auth P], LA [auth P], MA [auth Q], NA [auth R], OA [auth S], PA [auth T], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain JA [auth O] Focus chain KA [auth P] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain NA [auth R] Focus chain OA [auth S] Focus chain PA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain JA [auth O] Focus chain KA [auth P] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain NA [auth R] Focus chain OA [auth S] Focus chain PA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247 (Depositor), 0.251 (DCC)
R-Value Work: 0.196 (Depositor), 0.204 (DCC)
R-Value Observed: 0.199 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.298	α = 90
b = 104.419	β = 108.99
c = 171.124	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-12-07

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-12-07
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2023-09-20
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.