2DUU

Crystal Structure of apo-form of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp.

PDB DOI: https://doi.org/10.2210/pdb2DUU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-07-27 Released: 2006-09-05
Deposition Author(s): Kitatani, T., Nakamura, Y., Wada, K., Kinoshita, T., Tamoi, M., Shigeoka, S., Tada, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.275 (Depositor), 0.270 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942

Kitatani, T., Nakamura, Y., Wada, K., Kinoshita, T., Tamoi, M., Shigeoka, S., Tada, T.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 727-730

PubMed: 16880542 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309106027916
Primary Citation of Related Structures:
2DUU

PubMed Abstract:
The crystal structure of NADP-dependent apo-glyceraldehyde-3-phosphate dehydrogenase (apo-GAPDH) from Synechococcus PCC 7942 is reported. The crystal structure was solved by molecular replacement and refined to an R of 21.7% and R(free) of 27.5% at 2.9 angstroms resolution. The structural features of apo-GAPDH are as follows. The S-loop has an extremely flexible conformation and the sulfate ion is only taken into the classical P(i) site. A structural comparison with holo-GAPDHs indicated that the S-loop fixation is essential in the discrimination of NADP and NAD molecules.

Organizational Affiliation

Department of Applied Biochemistry, Graduate School of Agriculture and Life Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan.

Macromolecule Content

Total Structure Weight: 248.88 kDa
Atom Count: 15,053
Modelled Residue Count: 1,932
Deposited Residue Count: 2,280
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde 3-phosphate dehydrogenase	A B C [auth O] D [auth P] E [auth Q] A, B, C [auth O], D [auth P], E [auth Q], F [auth R]	380	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0 EC: 1.2.1.13 (PDB Primary Data), 1.2.1 (UniProt)
UniProt
Find proteins for Q9R6W2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q9R6W2 Go to UniProtKB: Q9R6W2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9R6W2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth O] SDF format, chain J [auth P] SDF format, chain K [auth Q] SDF format, chain L [auth R] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth O] MOL2 format, chain J [auth P] MOL2 format, chain K [auth Q] MOL2 format, chain L [auth R] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth O] mmCIF format, chain J [auth P] mmCIF format, chain K [auth Q] mmCIF format, chain L [auth R]	G [auth A] H [auth B] I [auth O] J [auth P] K [auth Q] G [auth A], H [auth B], I [auth O], J [auth P], K [auth Q], L [auth R]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth O] Focus chain J [auth P] Focus chain K [auth Q] Focus chain L [auth R] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth O] Focus chain J [auth P] Focus chain K [auth Q] Focus chain L [auth R]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.275 (Depositor), 0.270 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.4	α = 90
b = 79.8	β = 102.1
c = 207.2	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-09-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description