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- PDB-8iq7: Ambient Temperature Crystal Structure of Candida boidinii Formate... -

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Basic information

Entry
Database: PDB / ID: 8iq7
TitleAmbient Temperature Crystal Structure of Candida boidinii Formate Dehydrogenase
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / formate dehydrogenase / Candida boidinii / FDH / ambient temperature
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 species[Candida] boidinii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGul, M. / DeMirci, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography.
Authors: Gul, M. / Yuksel, B. / Bulut, H. / DeMirci, H.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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


Theoretical massNumber of molelcules
Total (without water)161,4604
Polymers161,4604
Non-polymers00
Water7,080393
1
A: Formate dehydrogenase
B: Formate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)80,7302
Polymers80,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-24 kcal/mol
Surface area27900 Å2
MethodPISA
2
C: Formate dehydrogenase
D: Formate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)80,7302
Polymers80,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-26 kcal/mol
Surface area27910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.668, 69.509, 110.800
Angle α, β, γ (deg.)77.86, 89.05, 81.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Formate dehydrogenase


Mass: 40364.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] boidinii (fungus) / Gene: FDH / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1EQY0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 5000 MME, 100 mM MES/Sodium hydroxide pH 6.5, 200 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Feb 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30.7 Å / Num. obs: 67168 / % possible obs: 85.9 % / Redundancy: 7.5 % / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.106 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4847 / CC1/2: 0.074 / CC star: 0.372 / Rpim(I) all: 0.481

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HTY

8hty


Resolution: 2.1→30.7 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 2000 2.98 %
Rwork0.2433 --
obs0.2441 67168 73.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11069 0 0 393 11462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211333
X-RAY DIFFRACTIONf_angle_d0.54515382
X-RAY DIFFRACTIONf_dihedral_angle_d13.9884168
X-RAY DIFFRACTIONf_chiral_restr0.0441731
X-RAY DIFFRACTIONf_plane_restr0.0041986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.4811010.43643298X-RAY DIFFRACTION52
2.15-2.210.4011070.40513477X-RAY DIFFRACTION54
2.21-2.280.39131080.38173516X-RAY DIFFRACTION55
2.28-2.350.39931150.34973754X-RAY DIFFRACTION59
2.35-2.430.3281200.33793912X-RAY DIFFRACTION62
2.43-2.530.36631260.32174102X-RAY DIFFRACTION64
2.53-2.650.35391300.29924247X-RAY DIFFRACTION66
2.65-2.780.33291420.28934637X-RAY DIFFRACTION73
2.78-2.960.30311520.25834936X-RAY DIFFRACTION78
2.96-3.190.27111650.23955387X-RAY DIFFRACTION84
3.19-3.510.24091760.20865718X-RAY DIFFRACTION90
3.51-4.010.20691790.17765850X-RAY DIFFRACTION92
4.01-5.050.1791890.15326147X-RAY DIFFRACTION96
5.05-30.70.18531900.17536187X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -1.6471 Å / Origin y: -0.4133 Å / Origin z: -0.8529 Å
111213212223313233
T0.1034 Å2-0.0255 Å2-0.005 Å2-0.0678 Å2-0.0294 Å2--0.0912 Å2
L0.2525 °2-0.129 °20.3403 °2-0.1047 °2-0.3078 °2--0.7282 °2
S-0.0088 Å °-0.0134 Å °0.0111 Å °0.0032 Å °-0.0071 Å °-0.014 Å °-0.0058 Å °-0.0048 Å °0.0088 Å °
Refinement TLS groupSelection details: all

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