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- PDB-4xye: GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+) -

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Basic information

Entry
Database: PDB / ID: 4xye
TitleGRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / FORMATE DEHYDROGENASE / NAD
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesGranulicella mallensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
B: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9464
Polymers85,6192
Non-polymers1,3272
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-53 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.050, 113.847, 115.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Formate dehydrogenase


Mass: 42809.738 Da / Num. of mol.: 2
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8NVB5, formate 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.: 778 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Mes pH 6.5, 12 % 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: 1.8→40.98 Å / Num. obs: 78950 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.2 / % possible all: 99.7

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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: 1.8→40.98 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 3659 5.04 %
Rwork0.1514 --
obs0.1531 72616 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5914 0 88 778 6780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076267
X-RAY DIFFRACTIONf_angle_d1.1648558
X-RAY DIFFRACTIONf_dihedral_angle_d13.0872326
X-RAY DIFFRACTIONf_chiral_restr0.078938
X-RAY DIFFRACTIONf_plane_restr0.0051112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82370.28671360.23992591X-RAY DIFFRACTION100
1.8237-1.84870.27541550.21772619X-RAY DIFFRACTION100
1.8487-1.87510.24431420.21162606X-RAY DIFFRACTION100
1.8751-1.90310.22771370.19382615X-RAY DIFFRACTION100
1.9031-1.93280.23451300.19032628X-RAY DIFFRACTION100
1.9328-1.96450.2461390.19242642X-RAY DIFFRACTION100
1.9645-1.99840.23911520.19512565X-RAY DIFFRACTION100
1.9984-2.03470.23011210.18222663X-RAY DIFFRACTION100
2.0347-2.07380.20941350.16912606X-RAY DIFFRACTION100
2.0738-2.11620.24721240.15352647X-RAY DIFFRACTION100
2.1162-2.16220.19471500.15182633X-RAY DIFFRACTION100
2.1622-2.21250.21741260.15222648X-RAY DIFFRACTION100
2.2125-2.26780.20321390.15742648X-RAY DIFFRACTION100
2.2678-2.32910.19191480.15892617X-RAY DIFFRACTION100
2.3291-2.39760.2221440.15572625X-RAY DIFFRACTION100
2.3976-2.4750.20971500.15072651X-RAY DIFFRACTION100
2.475-2.56350.17761530.14422643X-RAY DIFFRACTION100
2.5635-2.66610.16481370.13962633X-RAY DIFFRACTION100
2.6661-2.78740.1811370.14292676X-RAY DIFFRACTION100
2.7874-2.93430.18181280.14122678X-RAY DIFFRACTION100
2.9343-3.11810.15471460.14612674X-RAY DIFFRACTION100
3.1181-3.35870.18921500.14462651X-RAY DIFFRACTION100
3.3587-3.69660.18541260.14062725X-RAY DIFFRACTION100
3.6966-4.2310.14581660.12492681X-RAY DIFFRACTION100
4.231-5.32870.16761540.12432721X-RAY DIFFRACTION100
5.3287-40.99280.1331340.15462871X-RAY DIFFRACTION99

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