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- PDB-6d4b: Crystal structure of Candida boidinii formate dehydrogenase V123A... -

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Basic information

Entry
Database: PDB / ID: 6d4b
TitleCrystal structure of Candida boidinii formate dehydrogenase V123A mutant complexed with NAD+ and azide
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / 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 / mitochondrion / 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-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 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: 1.45 Å
AuthorsGuo, Q. / Ye, H. / Gakhar, L. / Cheatum, C.M. / Kohen, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM079368 United States
CitationJournal: Acs Catalysis / Year: 2019
Title: Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase
Authors: Pagano, P.L. / Guo, Q. / Ranasinghe, C. / Schroeder, E. / Robben, K. / Hase, F. / Ye, H. / Wickersham, K. / Aspuru-Guzik, A. / Major, D.T. / Gakhar, L. / Kohen, A. / Cheatum, C.M.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Formate dehydrogenase
B: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1568
Polymers80,6742
Non-polymers1,4826
Water20,6811148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-67 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.171, 116.098, 63.088
Angle α, β, γ (deg.)90.00, 106.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40336.918 Da / Num. of mol.: 2 / Mutation: V123A
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 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1148 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
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: RDI CMOS_8M / Detector: CMOS / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→44.937 Å / Num. obs: 122618 / % possible obs: 94.91 % / Redundancy: 3.5 % / Net I/σ(I): 15.5
Reflection shellResolution: 1.45→1.47 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALAdata scaling
XDSdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DN9

5dn9


Resolution: 1.45→44.937 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 17.78
RfactorNum. reflection% reflection
Rfree0.1803 11588 4.95 %
Rwork0.1538 --
obs0.1551 122618 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→44.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 96 1148 6876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085924
X-RAY DIFFRACTIONf_angle_d1.0428059
X-RAY DIFFRACTIONf_dihedral_angle_d16.3222181
X-RAY DIFFRACTIONf_chiral_restr0.078901
X-RAY DIFFRACTIONf_plane_restr0.0071030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.26123270.23646253X-RAY DIFFRACTION79
1.4665-1.48370.25863250.23436593X-RAY DIFFRACTION85
1.4837-1.50180.27533470.22397414X-RAY DIFFRACTION93
1.5018-1.52080.2263700.2157461X-RAY DIFFRACTION97
1.5208-1.54090.24233960.20167623X-RAY DIFFRACTION97
1.5409-1.5620.20774110.19967546X-RAY DIFFRACTION97
1.562-1.58430.2083590.20087604X-RAY DIFFRACTION97
1.5843-1.60790.22743940.19557608X-RAY DIFFRACTION97
1.6079-1.63310.21583360.19257685X-RAY DIFFRACTION98
1.6331-1.65980.24413900.19037468X-RAY DIFFRACTION96
1.6598-1.68850.20944170.18077272X-RAY DIFFRACTION94
1.6885-1.71920.22383390.17917294X-RAY DIFFRACTION93
1.7192-1.75220.2053840.17487319X-RAY DIFFRACTION93
1.7522-1.7880.19883850.1717259X-RAY DIFFRACTION94
1.788-1.82690.21614080.1647377X-RAY DIFFRACTION95
1.8269-1.86940.17724050.15937556X-RAY DIFFRACTION97
1.8694-1.91610.17733980.16087475X-RAY DIFFRACTION95
1.9161-1.96790.19174290.15087587X-RAY DIFFRACTION98
1.9679-2.02580.1823940.15237641X-RAY DIFFRACTION98
2.0258-2.09120.2053880.14817559X-RAY DIFFRACTION97
2.0912-2.1660.16094340.13597547X-RAY DIFFRACTION98
2.166-2.25270.16663830.13667611X-RAY DIFFRACTION97
2.2527-2.35520.16983710.13557629X-RAY DIFFRACTION97
2.3552-2.47940.18123510.13447604X-RAY DIFFRACTION98
2.4794-2.63470.15984070.1347621X-RAY DIFFRACTION97
2.6347-2.83810.17034130.14287509X-RAY DIFFRACTION96
2.8381-3.12360.16243980.14057458X-RAY DIFFRACTION96
3.1236-3.57550.17064400.13647260X-RAY DIFFRACTION94
3.5755-4.5040.1313710.1237249X-RAY DIFFRACTION93
4.504-44.95820.13944180.1317210X-RAY DIFFRACTION93

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