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- PDB-8bxx: Crystal structure of formate dehydrogenase FDH2 enzyme from Granu... -

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Basic information

Entry
Database: PDB / ID: 8bxx
TitleCrystal structure of formate dehydrogenase FDH2 enzyme from Granulicella mallensis MP5ACTX8 in complex with NAD and azide.
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
AZIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesGranulicella mallensis MP5ACTX8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsRobescu, M.S. / Rubini, R. / Filippini, F. / Bergantino, B. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
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: Rubini, R. / Robescu, M.S. / Tavanti, M. / Beneventi, E. / Lonigro, C. / Niero, M. / Zito, F. / Filippini, F. / Cendron, L. / Bergantino, E.
History
DepositionDec 10, 2022Deposition site: PDBE / Processing site: PDBE
SupersessionJan 18, 2023ID: 6T8J
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: Formate dehydrogenase
BB: Formate dehydrogenase
CC: Formate dehydrogenase
DD: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,42816
Polymers170,3584
Non-polymers3,07012
Water16,610922
1
AA: Formate dehydrogenase
DD: Formate dehydrogenase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 86.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)86,7148
Polymers85,1792
Non-polymers1,5356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-51 kcal/mol
Surface area26430 Å2
2
BB: Formate dehydrogenase
hetero molecules

CC: Formate dehydrogenase
hetero molecules


  • defined by author
  • 86.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)86,7148
Polymers85,1792
Non-polymers1,5356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10730 Å2
ΔGint-52 kcal/mol
Surface area26570 Å2
Unit cell
Length a, b, c (Å)72.066, 128.810, 85.664
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number4
Space group name H-MP1211

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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
Source: (gene. exp.) Granulicella mallensis MP5ACTX8 (bacteria)
Gene: AciX8_0868 / Production host: Escherichia coli (E. coli) / References: UniProt: G8NTI5, formate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-AZI / AZIDE ION


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 922 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0,1 M Ammonium Sulfate 0.1 M Bis-Tris pH 5.5 25% PEG 3350 5 mM NaN3, 10 mM NAD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.97→62.1 Å / Num. obs: 107087 / % possible obs: 97.83 % / Redundancy: 3.5 % / CC1/2: 0.913 / Net I/σ(I): 8.96
Reflection shellResolution: 1.97→2.04 Å / Mean I/σ(I) obs: 2.31 / Num. unique obs: 10633 / CC1/2: 0.551

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→62.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.234 --
Rwork0.188 --
obs-106070 97.83 %
Refinement stepCycle: LAST / Resolution: 1.97→62.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11540 0 204 922 12666

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