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- PDB-3fn4: Apo-form of NAD-dependent formate dehydrogenase from bacterium Mo... -

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Basic information

Entry
Database: PDB / ID: 3fn4
TitleApo-form of NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C-1 in closed conformation
ComponentsNAD-dependent formate dehydrogenase
KeywordsOXIDOREDUCTASE / homodimer / closed conformation of apo-form
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-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
Formate dehydrogenase
Similarity search - Component
Biological speciesMoraxella sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsShabalin, I.G. / Polyakov, K.M. / Filippova, E.V. / Dorovatovskiy, P.V. / Tikhonova, T.V. / Sadykhov, E.G. / Tishkov, V.I. / Popov, V.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structures of the apo and holo forms of formate dehydrogenase from the bacterium Moraxella sp. C-1: towards understanding the mechanism of the closure of the interdomain cleft
Authors: Shabalin, I.G. / Filippova, E.V. / Polyakov, K.M. / Sadykhov, E.G. / Safonova, T.N. / Tikhonova, T.V. / Tishkov, V.I. / Popov, V.O.
History
DepositionDec 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2563
Polymers44,0681
Non-polymers1882
Water1,74797
1
A: NAD-dependent formate dehydrogenase
hetero molecules

A: NAD-dependent formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5126
Polymers88,1352
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area8810 Å2
ΔGint-77 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.660, 66.089, 75.551
Angle α, β, γ (deg.)90.000, 104.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD-dependent formate dehydrogenase


Mass: 44067.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella sp. (bacteria) / Strain: C-1 / Gene: fdh / Plasmid: pMxFDH8a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: O08375, formate dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution (2mcl): 10.5 mg/ml FDH, 0.1M Na2HPO4 pH 7.0, Reservoir solution (2mcl): 0.1M HEPES pH 7.5, 2.2M Ammonium Sulfate, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.96→39.1 Å / Num. all: 27787 / Num. obs: 27648 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 2.4
Reflection shellResolution: 1.96→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3430 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
AUTOMARdata collection
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSD

2gsd


Resolution: 1.96→39.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.841 / SU B: 4.697 / SU ML: 0.127 / SU R Cruickshank DPI: 0.177 / SU Rfree: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1393 5 %RANDOM
Rwork0.187 ---
obs0.19 27648 99.53 %-
all-27787 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 58.6 Å2 / Biso mean: 32.438 Å2 / Biso min: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.83 Å2
2--0.34 Å20 Å2
3----0.99 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: LAST / Resolution: 1.96→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 11 97 3104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213089
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9574217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8835398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76723.438128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09715457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4271519
X-RAY DIFFRACTIONr_chiral_restr0.1260.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212373
X-RAY DIFFRACTIONr_mcbond_it1.0151.51982
X-RAY DIFFRACTIONr_mcangle_it1.70223176
X-RAY DIFFRACTIONr_scbond_it2.68731107
X-RAY DIFFRACTIONr_scangle_it3.9934.51041
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 100 -
Rwork0.338 1968 -
all-2068 -
obs--99.9 %

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