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- PDB-8j3o: Formate dehydrogenase wild-type enzyme from Candida dubliniensis ... -

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Basic information

Entry
Database: PDB / ID: 8j3o
TitleFormate dehydrogenase wild-type enzyme from Candida dubliniensis complexed with NADH
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / Formate dehydrogenase / Complex / NADH
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 / metal ion binding / cytosol
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesCandida dubliniensis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMa, W. / Zheng, Y.C. / Geng, Q. / Chen, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Chembiochem / Year: 2023
Title: Engineering a Formate Dehydrogenase for NADPH Regeneration.
Authors: Ma, W. / Geng, Q. / Chen, C. / Zheng, Y.C. / Yu, H.L. / Xu, J.H.
History
DepositionApr 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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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
C: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,73011
Polymers171,9964
Non-polymers2,7357
Water1,00956
1
A: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6642
Polymers42,9991
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area16290 Å2
MethodPISA
2
B: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6893
Polymers42,9991
Non-polymers6902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-18 kcal/mol
Surface area16260 Å2
MethodPISA
3
C: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6893
Polymers42,9991
Non-polymers6902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-18 kcal/mol
Surface area16510 Å2
MethodPISA
4
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6893
Polymers42,9991
Non-polymers6902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-17 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.402, 60.156, 120.482
Angle α, β, γ (deg.)90.00, 90.00, 111.02
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 42998.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) (yeast)
Gene: Cd36_53500, CD36_53500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9WHT3, formate dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 110 mM potassium thiocyanate, PEG2000MME, 33% (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.65→47.98 Å / Num. obs: 38451 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.944 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.141 / Rrim(I) all: 0.264 / Χ2: 0.98 / Net I/σ(I): 4.1 / Num. measured all: 134537
Reflection shellResolution: 2.65→2.77 Å / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.731 / Num. measured all: 17005 / Num. unique obs: 4684 / CC1/2: 0.687 / Rpim(I) all: 0.448 / Rrim(I) all: 0.859 / Χ2: 1.04 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→44.58 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 1790 4.66 %
Rwork0.2262 --
obs0.2286 38419 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11504 0 161 56 11721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611934
X-RAY DIFFRACTIONf_angle_d1.27216213
X-RAY DIFFRACTIONf_dihedral_angle_d8.3391641
X-RAY DIFFRACTIONf_chiral_restr0.0881802
X-RAY DIFFRACTIONf_plane_restr0.0122079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.36641690.30922809X-RAY DIFFRACTION97
2.72-2.80.31861270.29922786X-RAY DIFFRACTION97
2.8-2.890.40351280.32192837X-RAY DIFFRACTION98
2.89-30.38491000.29292828X-RAY DIFFRACTION98
3-3.120.31051240.28212769X-RAY DIFFRACTION98
3.12-3.260.33011270.28352834X-RAY DIFFRACTION98
3.26-3.430.31961670.26942805X-RAY DIFFRACTION98
3.43-3.640.25631360.2462819X-RAY DIFFRACTION98
3.64-3.920.25671310.21322815X-RAY DIFFRACTION98
3.92-4.320.25531650.19482831X-RAY DIFFRACTION99
4.32-4.940.26141600.17232809X-RAY DIFFRACTION99
4.94-6.230.26261270.20862843X-RAY DIFFRACTION99
6.23-44.580.21171290.17192844X-RAY DIFFRACTION98

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