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- PDB-2j6i: Candida boidinii formate dehydrogenase (FDH) C-terminal mutant -

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Basic information

Entry
Database: PDB / ID: 2j6i
TitleCandida boidinii formate dehydrogenase (FDH) C-terminal mutant
ComponentsFORMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / D-SPECIFIC-2- HYDROXY ACID DEHYDROGENASE / NAD+ DEPENDENT FORMATE DEHYDROGENASE / COFACTOR REGENERATOR / YEAST / CBFDH / CANDIDA BOIDINII
Function / homology
Function and homology information


methanol oxidation / formate catabolic process / methylamine metabolic process / formate dehydrogenase / choline catabolic process / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD+ binding / protein homodimerization activity / ATP 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
Formate dehydrogenase / Formate dehydrogenase
Similarity search - Component
Biological speciesCANDIDA BOIDINII (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchirwitz, K. / Schmidt, A. / Lamzin, V.S.
CitationJournal: Protein Sci. / Year: 2007
Title: High-Resolution Structures of Formate Dehydrogenase from Candida Boidinii.
Authors: Schirwitz, K. / Schmidt, A. / Lamzin, V.S.
History
DepositionSep 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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
C: FORMATE DEHYDROGENASE
D: FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3417
Polymers160,7594
Non-polymers5833
Water39,1832175
1
A: FORMATE DEHYDROGENASE
D: FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7684
Polymers80,3792
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FORMATE DEHYDROGENASE
C: FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5743
Polymers80,3792
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.360, 68.140, 109.150
Angle α, β, γ (deg.)78.07, 89.41, 81.27
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.446, 0.797, -0.407), (-0.837, 0.533, 0.127), (0.318, 0.284, 0.905)-2.858, -22.53, 52.66
2given(0.414, 0.877, -0.245), (0.875, -0.457, -0.158), (-0.25, -0.149, -0.9567)0.47, 1.09, -0.74

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Components

#1: Protein
FORMATE DEHYDROGENASE / NAD DEPENDENT FORMATE DEHYDROGENASE


Mass: 40189.656 Da / Num. of mol.: 4
Fragment: COFACTOR BINDING DOMAIN, CATALYTIC DOMAIN, RESIDUES 2-364
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA BOIDINII (fungus)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) 70034
Plasmid: PTRCHIS2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3)PLYS
References: UniProt: O93968, UniProt: O13437*PLUS, formate dehydrogenase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2175 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 328 TO VAL ENGINEERED RESIDUE IN CHAIN B, LYS 328 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, LYS 328 TO VAL ENGINEERED RESIDUE IN CHAIN B, LYS 328 TO VAL ENGINEERED RESIDUE IN CHAIN C, LYS 328 TO VAL ENGINEERED RESIDUE IN CHAIN D, LYS 328 TO VAL
Sequence detailsINITIAL METHIONINE REPLACED BY ALANINE. LYSINE 328 REPLACED BY VALINE.

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growpH: 6
Details: 0.1 M SODIUM-CACODYLATE PH 6.0 0.2 M AMMONIUM-SULPHATE 32.5 % W/V PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8031
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2005 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8031 Å / Relative weight: 1
ReflectionResolution: 1.55→19.5 Å / Num. obs: 196828 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12
Reflection shellResolution: 1.55→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NAC

2nac


Resolution: 1.55→19.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.378 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES GLY C 50 AND GLY D 50 ARE DISORDERED. RESIDUES 353-364 ARE MISSING IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 10365 5 %RANDOM
Rwork0.208 ---
obs0.21 196828 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.03 Å2-0.01 Å2
2---0.02 Å20.01 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10980 0 39 2175 13194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.95715434
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96451436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31124.922516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.414151934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9851552
X-RAY DIFFRACTIONr_chiral_restr0.0830.21734
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.26740
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.28003
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.21866
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.2122
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.276
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6541.57198
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.046211358
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67734687
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5054.54064
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.406 658
Rwork0.343 13120

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