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- PDB-4xyg: GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) -

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Basic information

Entry
Database: PDB / ID: 4xyg
TitleGRANULICELLA M. FORMATE DEHYDROGENASE (FDH)
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / FORMATE DEHYDROGENASE
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytoplasm
Similarity search - Function
NAD-dependent formate dehydrogenase / 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
Formate dehydrogenase
Similarity search - Component
Biological speciesGranulicella mallensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCendron, L. / Fogal, S. / Beneventi, E. / Bergantino, E.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Structural basis for double cofactor specificity in a new formate dehydrogenase from the acidobacterium Granulicella mallensis MP5ACTX8.
Authors: Fogal, S. / Beneventi, E. / Cendron, L. / Bergantino, E.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)42,8101
Polymers42,8101
Non-polymers00
Water6,828379
1
A: Formate dehydrogenase

A: Formate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)85,6192
Polymers85,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7280 Å2
ΔGint-39 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.166, 60.166, 179.683
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein Formate dehydrogenase


Mass: 42809.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8) (bacteria)
Gene: AciX8_2172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8NVB5, formate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01 M Nickel Chloride, 0.1 M TRIS pH 8.5, 20 %(w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→34.02 Å / Num. obs: 42594 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NAC

2nac


Resolution: 1.7→34.02 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 2142 5.04 %
Rwork0.1673 --
obs0.1687 42524 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 0 379 3285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072991
X-RAY DIFFRACTIONf_angle_d1.2084071
X-RAY DIFFRACTIONf_dihedral_angle_d12.5861095
X-RAY DIFFRACTIONf_chiral_restr0.082448
X-RAY DIFFRACTIONf_plane_restr0.009533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73960.24421480.2042655X-RAY DIFFRACTION100
1.7396-1.78310.22721430.19572613X-RAY DIFFRACTION100
1.7831-1.83130.23811340.18952674X-RAY DIFFRACTION100
1.8313-1.88520.27661530.18372638X-RAY DIFFRACTION100
1.8852-1.9460.20611620.17662631X-RAY DIFFRACTION100
1.946-2.01550.22161430.17972670X-RAY DIFFRACTION100
2.0155-2.09620.21231380.17212630X-RAY DIFFRACTION100
2.0962-2.19160.19281460.16692662X-RAY DIFFRACTION100
2.1916-2.30710.1921340.16662710X-RAY DIFFRACTION100
2.3071-2.45170.19041330.17432677X-RAY DIFFRACTION100
2.4517-2.64090.2051300.1752703X-RAY DIFFRACTION100
2.6409-2.90650.19941370.17332714X-RAY DIFFRACTION100
2.9065-3.32680.19481440.17392735X-RAY DIFFRACTION100
3.3268-4.19020.17291470.14822751X-RAY DIFFRACTION100

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