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- PDB-6t8c: Crystal structure of formate dehydrogenase FDH2 enzyme from Granu... -

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Basic information

Entry
Database: PDB / ID: 6t8c
TitleCrystal structure of formate dehydrogenase FDH2 enzyme from Granulicella mallensis MP5ACTX8 in the apo form.
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / formate dehydrogenase / NAD / 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 / cytosol
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / 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 domain superfamily
Similarity search - Domain/homology
Formate dehydrogenase
Similarity search - Component
Biological speciesGranulicella mallensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsRobescu, M.S. / Rubini, R. / Filippini, F. / Bergantino, B. / Cendron, L.
CitationJournal: Chemcatchem / Year: 2020
Title: From the Amelioration of a NADP+-dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice
Authors: Robescu, M.S. / Rubini, R. / Beneventi, E. / Tavanti, M. / Lonigro, C. / Zito, F. / Filippini, F. / Cendron, L. / Bergantino, E.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
C: Formate dehydrogenase
D: Formate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)170,3584
Polymers170,3584
Non-polymers00
Water13,818767
1
A: Formate dehydrogenase

D: Formate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)85,1792
Polymers85,1792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area7590 Å2
ΔGint-43 kcal/mol
Surface area28150 Å2
MethodPISA
2
B: Formate dehydrogenase
C: Formate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)85,1792
Polymers85,1792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-46 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.357, 112.492, 147.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Formate dehydrogenase / FDH / NAD-dependent formate dehydrogenase


Mass: 42589.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: aa not visible in the electron density maps are missing in the coordinates file
Source: (gene. exp.) Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8) (bacteria)
Strain: ATCC BAA-1857 / DSM 23137 / MP5ACTX8 / Gene: AciX8_0868 / Production host: Escherichia coli (E. coli) / References: UniProt: G8NTI5, formate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.97→48.95 Å / Num. obs: 636455 / % possible obs: 99.79 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.0453 / Net I/σ(I): 13.96
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 0.6385 / Mean I/σ(I) obs: 3.23 / Num. unique obs: 61436 / CC1/2: 0.71 / Rpim(I) all: 0.3057

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xyg

4xyg


Resolution: 1.97→48.95 Å / Cross valid method: THROUGHOUT
Num. reflection% reflectionSelection details
obs116749 99.79 %-
Rfree--RANDOM
Displacement parametersBiso max: 91.13 Å2 / Biso mean: 22.7362 Å2 / Biso min: 11 Å2
Refinement stepCycle: LAST / Resolution: 1.97→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11634 0 0 767 12401

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