1CF2 | pdb_00001cf2

THREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS FERVIDUS

PDB DOI: https://doi.org/10.2210/pdb1CF2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermus fervidus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-03-24 Released: 2000-03-29
Deposition Author(s): Charron, C., Talfournier, F., Isuppov, M.N., Branlant, G., Littlechild, J.A., Vitoux, B., Aubry, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.257 (Depositor)
R-Value Work:
0.194 (Depositor), 0.184 (DCC)

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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystallization and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus.

Charron, C., Talfournier, F., Isupov, M.N., Branlant, G., Littlechild, J.A., Vitoux, B., Aubry, A.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1353-1355

PubMed: 10393306 Search on PubMed
DOI: https://doi.org/10.1107/s0907444999005363
Primary Citation Related Structures:
1CF2

PubMed Abstract:
The homotetrameric holo-D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus has been crystallized in the presence of NADP+ using the hanging-drop vapour-diffusion method. Crystals grew from a solution containing 2-methyl-2,4-pentanediol and magnesium acetate. A native data set has been collected to 2.1 A using synchrotron radiation and cryocooling. Diffraction data have been processed in the orthorhombic system (space group P21212) with unit-cell dimensions a = 136.7, b = 153.3, c = 74.9 A and one tetramer per asymmetric unit.

Organizational Affiliation

Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, UPRESA CNRS 7036, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France.

Macromolecule Content

Total Structure Weight: 153.18 kDa
Atom Count: 11,620
Modeled Residue Count: 1,344
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)	A [auth P], B [auth R], C [auth O], D [auth Q]	337	Methanothermus fervidus	Mutation(s): 0 EC: 1.2.1.12 (PDB Primary Data), 1.2.1.59 (UniProt)
UniProt
Find proteins for P10618 (Methanothermus fervidus) Explore P10618 Go to UniProtKB: P10618
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain H [auth R] SDF format, chain J [auth O] SDF format, chain L [auth Q] SDF format, chain F [auth P] MOL2 format, chain H [auth R] MOL2 format, chain J [auth O] MOL2 format, chain L [auth Q] MOL2 format, chain F [auth P] mmCIF format, chain H [auth R] mmCIF format, chain J [auth O] mmCIF format, chain L [auth Q] mmCIF format, chain F [auth P]	F [auth P], H [auth R], J [auth O], L [auth Q]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain F [auth P] Focus chain H [auth R] Focus chain J [auth O] Focus chain L [auth Q] Interactions & Density Focus chain F [auth P] Focus chain H [auth R] Focus chain J [auth O] Focus chain L [auth Q]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth Q] SDF format, chain I [auth O] SDF format, chain G [auth R] SDF format, chain E [auth P] MOL2 format, chain K [auth Q] MOL2 format, chain I [auth O] MOL2 format, chain G [auth R] MOL2 format, chain E [auth P] mmCIF format, chain K [auth Q] mmCIF format, chain I [auth O] mmCIF format, chain G [auth R] mmCIF format, chain E [auth P]	E [auth P], G [auth R], I [auth O], K [auth Q]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth P] Focus chain G [auth R] Focus chain I [auth O] Focus chain K [auth Q] Interactions & Density Focus chain E [auth P] Focus chain G [auth R] Focus chain I [auth O] Focus chain K [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257 (Depositor)
R-Value Work: 0.194 (Depositor), 0.184 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.66	α = 90
b = 153.28	β = 90
c = 74.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-03-29
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2018-04-11
Changes: Data collection
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Derived calculations