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- PDB-2dbq: Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcu... -

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Basic information

Entry
Database: PDB / ID: 2dbq
TitleCrystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (I41)
ComponentsGlyoxylate reductase
KeywordsOXIDOREDUCTASE / glyoxylate reductase / D-3-phosphoglycerate dehydrogenase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


glyoxylate reductase / glyoxylate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol
Similarity search - Function
Glyoxylate reductase GyaR / 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 ...Glyoxylate reductase GyaR / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glyoxylate reductase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsYoshikawa, S. / Arai, R. / Kinoshita, Y. / Uchikubo-Kamo, T. / Akasaka, R. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Authors: Yoshikawa, S. / Arai, R. / Kinoshita, Y. / Uchikubo-Kamo, T. / Wakamatsu, T. / Akasaka, R. / Masui, R. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7359
Polymers38,3391
Non-polymers1,3968
Water6,846380
1
A: Glyoxylate reductase
hetero molecules

A: Glyoxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46918
Polymers76,6772
Non-polymers2,79216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area12660 Å2
ΔGint-125 kcal/mol
Surface area26260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.252, 114.252, 119.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Glyoxylate reductase / Glycolate reductase / PH0597


Mass: 38338.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0597 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: O58320, glyoxylate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 5.14 Å3/Da / Density % sol: 76.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0M Ammonium Sulfate, 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: 0.97892 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 27, 2005 / Details: two dimensional focusing mirror
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionRedundancy: 7.4 % / Number: 84158 / Rmerge(I) obs: 0.08 / Χ2: 1.006 / D res high: 1.7 Å / D res low: 50 Å / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665099.910.0530.9997.2
2.913.6610010.060.9997.5
2.542.9110010.0751.0027.5
2.312.5499.910.08817.5
2.142.3199.910.1011.0027.5
2.022.1410010.1251.0067.5
1.912.0210010.1711.0067.5
1.831.9110010.2381.0117.5
1.761.8310010.3441.0127.4
1.71.7699.810.4321.0236.5
ReflectionResolution: 1.7→50 Å / Num. obs: 84158 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.08 / Χ2: 1.006 / Net I/σ(I): 21.94
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.697 / Num. unique all: 8368 / Rsym value: 0.432 / Χ2: 1.023 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→36.29 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-K,-L) AND THE TWINNING FRACTION IS 0.3201. THE R-FACTOR IS 0.1318 AND THE R-FREE IS 0.1431 WHEN THIS TWINNING OPERATOR IS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1429 8071 9.75 %RANDOM
Rwork0.131 ---
obs-82804 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.508 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 19.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20 Å20 Å2
2--0.025 Å20 Å2
3----0.051 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 88 380 3141
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_angle_deg1.392
X-RAY DIFFRACTIONc_dihedral_angle_d22.29
X-RAY DIFFRACTIONc_improper_angle_d2.72
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.5972
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.5022.5
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.179 994 9.97 %
Rwork0.1852 8674 -
obs-9668 92.53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramPROTEIN.TOP
X-RAY DIFFRACTION2NAP.paramNAP.TOP
X-RAY DIFFRACTION3so4.paramSO4.TOP
X-RAY DIFFRACTION4water_rep.paramWATER.TOP
X-RAY DIFFRACTION5gol.paramGOL.TOP

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