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- PDB-1szj: STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM P... -

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Basic information

Entry
Database: PDB / ID: 1szj
TitleSTRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION
ComponentsD-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE / MOLECULAR SYMMETRY / ALLOSTERISM
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 / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPalinurus versicolor (painted spiny lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSong, S. / Li, J. / Lin, Z.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Preliminary crystallographic studies of lobster D-glyceraldehyde-3-phosphate dehydrogenase and the modified enzyme carrying the fluorescent derivative.
Authors: Song, S.Y. / Gao, Y.G. / Zhou, J.M. / Tsou, C.L.
#1: Journal: Arch.Biochem.Biophys. / Year: 1993
Title: Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase from Palinurus Versicolor Carrying the Fluorescent Nad Derivatives at 2.7 A Resolution
Authors: Lin, Z.J. / Li, J. / Zhang, F.M. / Song, S.Y. / Yang, J. / Liang, S.J. / Tsou, C.L.
History
DepositionFeb 4, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2458
Polymers71,5342
Non-polymers1,7116
Water6,593366
1
G: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
R: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)146,49016
Polymers143,0684
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21010 Å2
ΔGint-270 kcal/mol
Surface area43060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.400, 99.900, 80.790
Angle α, β, γ (deg.)90.00, 114.48, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99997, -0.00521, -0.0049), (0.00521, -0.99999, 0.00067), (-0.0049, 0.00064, 0.99999)
Vector: -0.03693, 0.06745, 0.10541)

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Components

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


Mass: 35767.004 Da / Num. of mol.: 2 / Fragment: NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN / Source method: isolated from a natural source / Details: COMPLEX WITH NAD+
Source: (natural) Palinurus versicolor (painted spiny lobster)
Organ: TAIL / Tissue: TAIL MUSCLE
References: UniProt: P56649, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3.27 Å3/Da / Density % sol: 62 %
Description: THE 2.7 ANGSTROM STRUCTURE OF IRR-GAPDH FROM PALINURUS VERSICOLOR WAS DETERMINED BY MOLECULAR REPLACEMENT USING HOMARUS AMERICANUS HOLO-GAPDH AS A SEARCH MODEL.
Crystal growTemperature: 280 K / pH: 6.1
Details: THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULPHATE IN 0.1M PHOSPHATE BUFFER (PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2. ...Details: THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULPHATE IN 0.1M PHOSPHATE BUFFER (PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULPHATE IN SAME BUFFER. THE CRYSTALLIZATION WAS CARRIED OUT AT 280K.

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 1, 1994
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 84900 / % possible obs: 83.5 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 3.9
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 1.6 / % possible all: 56.5

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMARUS AMERICANUS HOLO-GAPDH

Resolution: 2→6 Å / Data cutoff low absF: 50 / σ(F): 3
Details: DURING THE REFINEMENT, NO NCS RESTRAINTS WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 5073 11.28 %RANDOM
Rwork0.168 ---
obs0.168 49184 81.64 %-
Displacement parametersBiso mean: 32.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 108 366 5486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.98→2.09 Å
RfactorNum. reflection% reflection
Rfree0.2813 470 11.26 %
Rwork0.254 44985 -
obs--44.65 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD

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