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- PDB-5dna: Crystal structure of Candida boidinii formate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 5dna
TitleCrystal structure of Candida boidinii formate dehydrogenase
ComponentsFORMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / isozyme / recombinant
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 dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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-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 dehydrogenase, NAD-binding domain conserved site 1 / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Formate dehydrogenase
Similarity search - Component
Biological speciesCandida boidinii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGuo, Q. / Gakhar, L. / Wichersham, K. / Francis, K. / Vardi-Kilshtain, A. / Major, D.T. / Cheatum, C.M. / Kohen, A.
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.
Authors: Guo, Q. / Gakhar, L. / Wickersham, K. / Francis, K. / Vardi-Kilshtain, A. / Major, D.T. / Cheatum, C.M. / Kohen, A.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,9409
Polymers161,4604
Non-polymers4805
Water32,0131777
1
A: FORMATE DEHYDROGENASE
B: FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0185
Polymers80,7302
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-51 kcal/mol
Surface area27570 Å2
MethodPISA
2
C: FORMATE DEHYDROGENASE
D: FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9224
Polymers80,7302
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-45 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.711, 68.514, 109.458
Angle α, β, γ (deg.)78.11, 89.66, 81.24
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A1EQY0, formate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1777 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium acetate trihydrate, 0.1 M HEPES, 25% PEG 4000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→19.9 Å / Num. obs: 141899 / % possible obs: 93.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.3
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.9 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
REFMACrefinement
Cootmodel building
XDSdata reduction
PHASERphasing
StructureStudiodata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6I

2j6i


Resolution: 1.75→19.895 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 7199 5.07 %
Rwork0.1433 --
obs0.1453 141888 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→19.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11038 0 25 1777 12840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111333
X-RAY DIFFRACTIONf_angle_d1.26615387
X-RAY DIFFRACTIONf_dihedral_angle_d13.2374165
X-RAY DIFFRACTIONf_chiral_restr0.0551731
X-RAY DIFFRACTIONf_plane_restr0.0071978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.26381960.21294321X-RAY DIFFRACTION89
1.7699-1.79070.27362290.21484421X-RAY DIFFRACTION90
1.7907-1.81250.24372330.20574267X-RAY DIFFRACTION90
1.8125-1.83540.26922230.20134369X-RAY DIFFRACTION90
1.8354-1.85960.22042530.18344367X-RAY DIFFRACTION91
1.8596-1.8850.22942240.18144316X-RAY DIFFRACTION91
1.885-1.91190.26112530.18194461X-RAY DIFFRACTION91
1.9119-1.94040.22082190.17534360X-RAY DIFFRACTION91
1.9404-1.97070.21372320.16414416X-RAY DIFFRACTION92
1.9707-2.0030.20272630.16124398X-RAY DIFFRACTION92
2.003-2.03750.18652370.15664427X-RAY DIFFRACTION92
2.0375-2.07450.20112360.15364534X-RAY DIFFRACTION93
2.0745-2.11440.192310.1484417X-RAY DIFFRACTION93
2.1144-2.15750.18442500.13964456X-RAY DIFFRACTION93
2.1575-2.20440.19262390.13384481X-RAY DIFFRACTION93
2.2044-2.25560.19452370.13664486X-RAY DIFFRACTION94
2.2556-2.31190.17712300.13684534X-RAY DIFFRACTION94
2.3119-2.37430.19152250.1354570X-RAY DIFFRACTION94
2.3743-2.44410.17342800.13534561X-RAY DIFFRACTION94
2.4441-2.52280.2022520.13574507X-RAY DIFFRACTION95
2.5228-2.61280.17642600.13724558X-RAY DIFFRACTION95
2.6128-2.71710.1932260.14214613X-RAY DIFFRACTION95
2.7171-2.84050.18852470.14774643X-RAY DIFFRACTION96
2.8405-2.98970.18112440.14684625X-RAY DIFFRACTION96
2.9897-3.17640.20372350.14664648X-RAY DIFFRACTION97
3.1764-3.42050.17612600.14224652X-RAY DIFFRACTION97
3.4205-3.76260.1622630.12544657X-RAY DIFFRACTION97
3.7626-4.30230.13272370.11624659X-RAY DIFFRACTION97
4.3023-5.40230.12522490.10794594X-RAY DIFFRACTION95
5.4023-19.89580.14612360.14244371X-RAY DIFFRACTION91

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