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- PDB-6t9w: Crystal structure of formate dehydrogenase FDH2 D222A/Q223R enzym... -

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Basic information

Entry
Database: PDB / ID: 6t9w
TitleCrystal structure of formate dehydrogenase FDH2 D222A/Q223R enzyme from Granulicella mallensis MP5ACTX8 in complex with NADP 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Formate dehydrogenase
Similarity search - Component
Biological speciesGranulicella mallensis MP5ACTX8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 29, 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
B: Formate dehydrogenase
A: Formate dehydrogenase
C: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,65510
Polymers170,2984
Non-polymers2,3566
Water13,421745
1
B: Formate dehydrogenase
hetero molecules

C: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7206
Polymers85,1492
Non-polymers1,5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area10470 Å2
ΔGint-58 kcal/mol
Surface area26670 Å2
MethodPISA
2
A: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9354
Polymers85,1492
Non-polymers7852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-48 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.530, 62.080, 211.745
Angle α, β, γ (deg.)90.000, 91.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42574.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: not assigned coordinates correspond to not atoms not visible in the electron density
Source: (gene. exp.) Granulicella mallensis MP5ACTX8 (bacteria)
Gene: AciX8_0868 / Production host: Escherichia coli (E. coli) / References: UniProt: G8NTI5, formate dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Citrate pH 5.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→70.65 Å / Num. obs: 153758 / % possible obs: 99.1 % / Redundancy: 4.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.3
Reflection shellResolution: 2.15→70.56 Å / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2 / Num. unique obs: 3923 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T8C

6t8c


Resolution: 2.15→54.1 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2307 --
Rwork0.1912 --
obs-146071 87.71 %
Displacement parametersBiso max: 167.86 Å2 / Biso mean: 25.6723 Å2 / Biso min: 4.89 Å2
Refinement stepCycle: LAST / Resolution: 2.15→54.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11826 0 153 745 12724

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