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- PDB-1qp8: CRYSTAL STRUCTURE OF A PUTATIVE FORMATE DEHYDROGENASE FROM PYROBA... -

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Basic information

Entry
Database: PDB / ID: 1qp8
TitleCRYSTAL STRUCTURE OF A PUTATIVE FORMATE DEHYDROGENASE FROM PYROBACULUM AEROPHILUM
ComponentsFORMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SIMILAR TO THE PREVIOUSLY SOLVED FORMATE DEHYDROGENASE
Function / homology
Function and homology information


hydroxypyruvate reductase activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol
Similarity search - Function
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
Chem-NDP / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsPeat, T.S. / Newman, J. / Waldo, G.S. / Terwilliger, T.C.
CitationJournal: To be Published
Title: The Crystal Structure of a Putative Formate Dehydrogenase from Pyrobaculum Aerophilum
Authors: Peat, T.S. / Newman, J. / Waldo, G.S. / Terwilliger, T.C.
History
DepositionJun 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMATE DEHYDROGENASE
B: FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7983
Polymers68,0522
Non-polymers7451
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-31 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.760, 101.760, 212.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe asymmetric unit has two molecules, A and B. The A molecule is bound to NADP, whereas there is no density for the NADP in the B molecule. The A molecule is also much better ordered than the B molecule in the small domain.

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Components

#1: Protein FORMATE DEHYDROGENASE /


Mass: 34026.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FULL LENGTH PROTEIN WITH C-TERM HIS TAG (HHHHHH). HIS TAG WAS NOT SEEN IN THE DENSITY.
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Description: hyperthermophilic archeabacterium / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZXP5
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.05 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: about 3M formate at pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 28370 / Num. obs: 28352 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→3 Å / Redundancy: 16 % / Rmerge(I) obs: 0.31 / Num. unique all: 4754 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.8→50 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The bulk solvent was used as implemented in CNS.
RfactorNum. reflection% reflection
Rfree0.32 1417 5 %
Rwork0.274 --
all0.274 28370 -
obs0.274 28352 99.9 %
Displacement parametersBiso mean: 59.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 48 3 4791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.7

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