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- PDB-8oq2: Binding of NADP to a formate dehydrogenase from Starkeya novella. -

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Basic information

Entry
Database: PDB / ID: 8oq2
TitleBinding of NADP to a formate dehydrogenase from Starkeya novella.
ComponentsFormate dehydrogenase
KeywordsSTRUCTURAL PROTEIN / Mutant / dehydrogenase
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 dehydrogenases signature 2. / 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 speciesStarkeya novella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsPartipilo, M. / Whittaker, J.J. / Pontillo, N. / Guskov, A. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.003.019 Netherlands
CitationJournal: To Be Published
Title: Binding of NADP to a formate dehydrogenase from Starkeya novella.
Authors: Partipilo, M. / Whittaker, J.J. / Pontillo, N. / Coenradij, J. / Herrmann, A. / Guskov, A. / Slotboom, D.J.
History
DepositionApr 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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
E: Formate dehydrogenase
F: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,17926
Polymers252,1306
Non-polymers5,04920
Water2,504139
1
A: Formate dehydrogenase
B: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,82411
Polymers84,0432
Non-polymers1,7819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-44 kcal/mol
Surface area25590 Å2
MethodPISA
2
C: Formate dehydrogenase
F: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,82411
Polymers84,0432
Non-polymers1,7819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-47 kcal/mol
Surface area25920 Å2
MethodPISA
3
D: Formate dehydrogenase
hetero molecules

E: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5304
Polymers84,0432
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_664y+1,-x+y+1,z-1/61
Buried area10240 Å2
ΔGint-42 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.265, 132.265, 302.952
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 42021.715 Da / Num. of mol.: 6 / Mutation: A198G, D221Q, H379K, S380V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Starkeya novella (bacteria) / Gene: Snov_3272 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D7A8L2, formate dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: Citric acid pH 4.5, PEG 3350, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.91→114.6 Å / Num. obs: 163262 / % possible obs: 82 % / Redundancy: 8 % / Biso Wilson estimate: 35.7 Å2 / CC1/2: 0.91 / Net I/σ(I): 12
Reflection shellResolution: 1.91→7.2 Å / Num. unique obs: 3586 / CC1/2: 0.76 / % possible all: 25.54

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→114.6 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.275 --0.2961
Rwork0.2374 ---
obs-92372 99.44 %-
Refinement stepCycle: LAST / Resolution: 1.91→114.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18072 0 0 139 18211

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