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- PDB-2czc: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 2czc
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii OT3
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Glycolysis / NAD / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / 4-hydroxy-tetrahydrodipicolinate reductase / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / lysine biosynthetic process via diaminopimelate / glycolytic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type II / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 ...Glyceraldehyde-3-phosphate dehydrogenase, type II / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIto, K. / Arai, R. / Kamo-Uchikubo, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii OT3
Authors: Ito, K. / Arai, R. / Kamo-Uchikubo, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,38013
Polymers149,2514
Non-polymers3,1299
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-137 kcal/mol
Surface area42990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.693, 127.192, 161.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailstetramer (A, B, C, D)

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / NADP / -dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 37312.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1830 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CodonPlus-RIL
References: UniProt: O59494, glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris(pH8.0), 18% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 26, 2005 / Details: Two dimensional focusing mirror
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 88750 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.43 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.079 / Net I/σ(I): 13.21
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.03 / Num. unique all: 6773 / Rsym value: 0.432 / % possible all: 73.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CF2

1cf2


Resolution: 2→49.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 469187.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 8375 10 %RANDOM
Rwork0.205 ---
obs-83684 88.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1697 Å2 / ksol: 0.377327 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20 Å20 Å2
2--4.73 Å20 Å2
3----2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10474 0 201 478 11153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.131.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it3.272
X-RAY DIFFRACTIONc_scangle_it3.992.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 1079 10.2 %
Rwork0.268 9531 -
obs-10186 67.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2po4_prodrg.parampo4_prodrg.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4nad_prodrg.paramnad_prodrg.top

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