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- PDB-4xyb: GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NADP(... -

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Basic information

Entry
Database: PDB / ID: 4xyb
TitleGRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NADP(+) AND NaN3
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / FORMATE DEHYDROGENASE / NADP
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
AZIDE ION / Chem-NDP / Formate dehydrogenase
Similarity search - Component
Biological speciesGranulicella mallensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)87,50511
Polymers85,6192
Non-polymers1,8859
Water17,312961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-30 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.056, 113.804, 116.191
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)
Strain: ATCC BAA-1857 / DSM 23137 / MP5ACTX8 / Gene: AciX8_2172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8NVB5, formate dehydrogenase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Na Acetate 2.0 M Formate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2012 / Details: Focusing optics: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.38→40.64 Å / Num. obs: 154449 / % possible obs: 97.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.25 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.2
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.4 / % possible all: 82.4

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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 / Resolution: 1.38→31 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.156 7741 5.02 %
Rwork0.1407 --
obs0.1414 154343 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5914 0 122 961 6997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066203
X-RAY DIFFRACTIONf_angle_d1.158444
X-RAY DIFFRACTIONf_dihedral_angle_d11.9812297
X-RAY DIFFRACTIONf_chiral_restr0.076923
X-RAY DIFFRACTIONf_plane_restr0.0061110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.39570.18542130.16473839X-RAY DIFFRACTION78
1.3957-1.41210.18752040.15924050X-RAY DIFFRACTION82
1.4121-1.42930.17521900.15184382X-RAY DIFFRACTION88
1.4293-1.44740.15932440.14854527X-RAY DIFFRACTION91
1.4474-1.46650.15782440.1454629X-RAY DIFFRACTION93
1.4665-1.48660.15952740.14044771X-RAY DIFFRACTION96
1.4866-1.50780.17532580.13844845X-RAY DIFFRACTION98
1.5078-1.53030.15382460.12844949X-RAY DIFFRACTION99
1.5303-1.55420.15892650.1284927X-RAY DIFFRACTION100
1.5542-1.57970.13422500.12375011X-RAY DIFFRACTION100
1.5797-1.60690.14382670.12474969X-RAY DIFFRACTION100
1.6069-1.63610.14972320.12574987X-RAY DIFFRACTION100
1.6361-1.66760.14812510.12695020X-RAY DIFFRACTION100
1.6676-1.70160.14492700.12814971X-RAY DIFFRACTION100
1.7016-1.73860.14252900.13114920X-RAY DIFFRACTION100
1.7386-1.77910.15172470.1345053X-RAY DIFFRACTION100
1.7791-1.82360.1612690.13544956X-RAY DIFFRACTION100
1.8236-1.87290.15182690.13425019X-RAY DIFFRACTION100
1.8729-1.9280.14442510.13264972X-RAY DIFFRACTION100
1.928-1.99020.15112640.13545016X-RAY DIFFRACTION100
1.9902-2.06130.15252600.14015038X-RAY DIFFRACTION100
2.0613-2.14380.15762860.13474977X-RAY DIFFRACTION100
2.1438-2.24140.14342620.13615039X-RAY DIFFRACTION100
2.2414-2.35950.15552390.14315053X-RAY DIFFRACTION100
2.3595-2.50730.17172840.14975019X-RAY DIFFRACTION100
2.5073-2.70080.16232800.15085046X-RAY DIFFRACTION100
2.7008-2.97230.15292650.15075067X-RAY DIFFRACTION100
2.9723-3.4020.16873020.15365070X-RAY DIFFRACTION100
3.402-4.28430.14682810.13245130X-RAY DIFFRACTION100
4.2843-31.00820.15952840.15035350X-RAY DIFFRACTION100

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