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- PDB-1wwk: Crystal structure of phosphoglycerate dehydrogenase from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 1wwk
TitleCrystal structure of phosphoglycerate dehydrogenase from Pyrococcus horikoshii OT3
Componentsphosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / phosphoglycerate dehydrogenase / Pyrococcus horikoshii / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / 307aa long hypothetical phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of phosphoglycerate dehydrogenase from Pyrococcus horikoshii OT3
Authors: Sugahara, M. / Kunishima, N.
History
DepositionJan 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: phosphoglycerate dehydrogenase
B: phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7354
Polymers67,4092
Non-polymers1,3272
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-34 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.417, 46.163, 66.258
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein phosphoglycerate dehydrogenase


Mass: 33704.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: GenBank: 14591190, UniProt: O50095*PLUS, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 546 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.7 / Details: PEG4000, NAD, pH 5.7, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
ROTATING ANODERIGAKU21.54178
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEDec 13, 2004
RIGAKU RAXIS IV2IMAGE PLATEDec 3, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1MIRRORS
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541781
ReflectionResolution: 1.9→40 Å / Num. all: 53427 / Num. obs: 53427 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 26.28 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.051 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5263 / Rsym value: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.9→37.48 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2735 -RANDOM
Rwork0.224 ---
obs0.224 53427 99.8 %-
all-53427 --
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20 Å2-5.43 Å2
2---0.92 Å20 Å2
3----1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 88 546 5298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.011
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.271 251 -
Rwork0.28 --
obs-4982 99.2 %

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