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- PDB-1crw: CRYSTAL STRUCTURE OF APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE... -

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Basic information

Entry
Database: PDB / ID: 1crw
TitleCRYSTAL STRUCTURE OF APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR AT 2.0A RESOLUTION
ComponentsD-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / FREE-NAD GAPDH
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPalinurus versicolor (painted spiny lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsShen, Y. / Li, J. / Song, S. / Lin, Z.
Citation
Journal: J.Struct.Biol. / Year: 2000
Title: Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.
Authors: Shen, Y.Q. / Li, J. / Song, S.Y. / Lin, Z.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of Holo-Glyceraldehyde-3-phosphate Dehydrogenase from Palinurus Versicolor Refined at 2A Resolution
Authors: Song, S. / Li, J. / Lin, Z.
History
DepositionAug 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 7, 2021Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
R: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)71,5342
Polymers71,5342
Non-polymers00
Water5,855325
1
G: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
R: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE

G: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
R: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)143,0684
Polymers143,0684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14470 Å2
ΔGint-99 kcal/mol
Surface area44540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.45, 99.84, 80.79
Angle α, β, γ (deg.)90, 115.14, 90
Int Tables number5
Space group name H-MC121
DetailsThe biological tetramer is obtained by the two-fold symmetry operation of chain G and chain R.

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Components

#1: Protein D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE


Mass: 35767.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Palinurus versicolor (painted spiny lobster)
Tissue: TAIL MUSCLE
References: UniProt: P56649, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Crystal grow
*PLUS
Details: Song, S.Y., (1988) Sci. Chin., 3, 313.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 10, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 154634 / Num. obs: 54995 / Observed criterion σ(F): 0 / Redundancy: 1.4 % / Rmerge(I) obs: 0.0706
Reflection shellHighest resolution: 1.8 Å / Num. unique all: 54995
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 45695 / % possible obs: 74.5 % / Num. measured all: 136230

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
WEISdata reduction
WEISdata scaling
X-PLORphasing
RefinementResolution: 2→6 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4206 -RANDOM
Rwork0.165 ---
all-54995 --
obs-41698 74.5 %-
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 0 325 5337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_d2.87
X-RAY DIFFRACTIONx_angle_deg25.68
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.26

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