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- PDB-1dss: STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHO... -

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Basic information

Entry
Database: PDB / ID: 1dss
TitleSTRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR
ComponentsD-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
KeywordsACTIVE-SITE CARBOXYMETHYLATION / D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE / 'THE-HALF-OF-SITES' REACTION / MOLECULAR SYMMETRY
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, 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: 1.88 Å
AuthorsSong, S. / Lin, Z.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.
Authors: Song, S.Y. / Xu, Y.B. / Lin, Z.J. / 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.
#2: 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.
History
DepositionJun 4, 1997Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)73,3618
Polymers71,6502
Non-polymers1,7116
Water7,206400
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)146,72216
Polymers143,3004
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21340 Å2
ΔGint-299 kcal/mol
Surface area41770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.100, 99.610, 80.690
Angle α, β, γ (deg.)90.00, 114.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99994, -0.00796, -0.00711), (0.00793, -0.99996, 0.00424), (-0.00714, 0.00418, 0.99997)
Vector: -0.07499, -0.01091, 0.12243)

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Components

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


Mass: 35825.039 Da / Num. of mol.: 2 / Fragment: NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN / Source method: isolated from a natural source / Details: NAD+
Source: (natural) Palinurus versicolor (painted spiny lobster)
Organ: TAIL MUSCLE
References: UniProt: P56649, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / 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


Mass: 18.015 Da / Num. of mol.: 400 / 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 %
Crystal growTemperature: 290 K / pH: 6.1
Details: THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULFATE IN 0.1M PHOSPHATE BUFFER(PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M ...Details: THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULFATE IN 0.1M PHOSPHATE BUFFER(PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULFATE IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C., temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion / Details: Song, S.Y., (1983) J.Mol.Biol., 171, 225.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMNAD+1drop
21.0 mMEDTA1drop
31.6 Mammonium sulfate1drop
40.1 Mphosphate1drop
50.035 mMenzyme1drop
62.7 Mammonium sulfate1reservoir
70.1 Mphosphate1reservoir

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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: Nov 1, 1990
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→150 Å / Num. obs: 78030 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 1.07 % / Biso Wilson estimate: 14.73 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 4.2
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 1.07 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 2.1 / % possible all: 56.5
Reflection shell
*PLUS
% possible obs: 56.5 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
WEISdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOLO-GAPDH FROM PALINURUS VERSICOLOR (2.0A)

Resolution: 1.88→6 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 70 / Cross valid method: THROUGHOUT / σ(F): 3
Details: DURING THE REFINEMENT, NO NCS RESTRAINTS WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5961 10.15 %RANDOM
Rwork0.1717 ---
obs0.1717 58730 80.96 %-
Displacement parametersBiso mean: 17.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.88→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 108 400 5528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.65
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_d1.79
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: 1.88→1.96 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.282 462 8.34 %
Rwork0.2666 4019 -
obs--49.73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19CM.PROTOPH19CM.PRO
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.79
LS refinement shell
*PLUS
Rfactor obs: 0.2666

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