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- PDB-5dn9: Crystal structure of Candida boidinii formate dehydrogenase compl... -

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Basic information

Entry
Database: PDB / ID: 5dn9
TitleCrystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide
ComponentsFDH
KeywordsOXIDOREDUCTASE / transition state / ternary complex
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 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
AZIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesCandida boidinii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGuo, Q. / Gakhar, L. / Wichersham, K. / Francis, K. / Vardi-Kilshtain, A. / Major, D.T. / Cheatum, C.M. / Kohen, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065368 United States
National Science Foundation (NSF, United States)CHE-1149023 United States
United States - Israel Binational Science Foundation (BSF)2012340 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079368 United States
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 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
A: FDH
B: FDH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2128
Polymers80,7302
Non-polymers1,4826
Water19,5281084
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-66 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.931, 116.617, 63.208
Angle α, β, γ (deg.)90.00, 106.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FDH


Mass: 40364.969 Da / Num. of mol.: 2
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1084 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 25% PEG 3000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 23, 2013
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→41.98 Å / Num. obs: 107639 / % possible obs: 95.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.4 / % possible all: 88.5

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Processing

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

2j6i


Resolution: 1.5→41.976 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 15.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1691 10639 4.99 %
Rwork0.1383 --
obs0.1398 107560 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→41.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5636 0 96 1084 6816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095886
X-RAY DIFFRACTIONf_angle_d1.2888003
X-RAY DIFFRACTIONf_dihedral_angle_d13.1592163
X-RAY DIFFRACTIONf_chiral_restr0.073899
X-RAY DIFFRACTIONf_plane_restr0.0071018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4987-1.51580.25552840.24534985X-RAY DIFFRACTION72
1.5158-1.53360.29233330.23996293X-RAY DIFFRACTION89
1.5336-1.55230.2593750.20146622X-RAY DIFFRACTION94
1.5523-1.57190.2233320.18626693X-RAY DIFFRACTION95
1.5719-1.59260.23413900.18896894X-RAY DIFFRACTION96
1.5926-1.61440.21573400.18696677X-RAY DIFFRACTION96
1.6144-1.63750.20563760.17376849X-RAY DIFFRACTION96
1.6375-1.6620.19683620.16956746X-RAY DIFFRACTION96
1.662-1.68790.21143860.16736814X-RAY DIFFRACTION96
1.6879-1.71560.20183350.16346882X-RAY DIFFRACTION96
1.7156-1.74520.17613710.14986795X-RAY DIFFRACTION97
1.7452-1.77690.19183230.14816818X-RAY DIFFRACTION96
1.7769-1.81110.16323310.14586981X-RAY DIFFRACTION97
1.8111-1.84810.18413380.14266808X-RAY DIFFRACTION97
1.8481-1.88830.19953520.14596855X-RAY DIFFRACTION97
1.8883-1.93220.16763590.14416800X-RAY DIFFRACTION97
1.9322-1.98050.18463840.13626918X-RAY DIFFRACTION97
1.9805-2.0340.18663640.14386841X-RAY DIFFRACTION97
2.034-2.09390.17793670.14266890X-RAY DIFFRACTION97
2.0939-2.16150.17243560.13236866X-RAY DIFFRACTION97
2.1615-2.23870.15973830.12596809X-RAY DIFFRACTION97
2.2387-2.32840.16663600.1236897X-RAY DIFFRACTION97
2.3284-2.43430.1513590.12096943X-RAY DIFFRACTION98
2.4343-2.56260.14944020.12066858X-RAY DIFFRACTION98
2.5626-2.72320.16043700.12656895X-RAY DIFFRACTION97
2.7232-2.93340.15613620.13016853X-RAY DIFFRACTION97
2.9334-3.22850.15573280.12666901X-RAY DIFFRACTION97
3.2285-3.69540.13623660.12316775X-RAY DIFFRACTION96
3.6954-4.65490.13543070.11116848X-RAY DIFFRACTION96
4.6549-41.99270.13533440.1286854X-RAY DIFFRACTION97

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