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- PDB-6jx1: Crystal structure of Formate dehydrogenase mutant V198I/C256I/P26... -

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Basic information

Entry
Database: PDB / ID: 6jx1
TitleCrystal structure of Formate dehydrogenase mutant V198I/C256I/P260S/E261P/S381N/S383F from Pseudomonas sp. 101
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / Formate Dehydrogenase
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 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 speciesPseudomonas sp. 101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.233 Å
AuthorsFeng, Y. / Xue, S. / Guo, X. / Zhao, Z.
CitationJournal: Chemistry / Year: 2020
Title: Structure-Guided Design of Formate Dehydrogenase for Regeneration of a Non-Natural Redox Cofactor.
Authors: Guo, X. / Wang, X. / Liu, Y. / Li, Q. / Wang, J. / Liu, W. / Zhao, Z.K.
History
DepositionApr 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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)88,6193
Polymers88,5262
Non-polymers921
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-40 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.496, 53.910, 117.063
Angle α, β, γ (deg.)90.00, 121.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44263.215 Da / Num. of mol.: 2 / Mutation: V198I/C256I/H260S/E261P/S381N/S383F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. 101 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33160, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 27557 / % possible obs: 74.62 % / Redundancy: 2.7 % / Biso Wilson estimate: 28.54 Å2 / CC1/2: 0.879 / Rmerge(I) obs: 0.23 / Net I/av σ(I): 4.33 / Net I/σ(I): 4.33
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 1285 / CC1/2: 0.908 / % possible all: 35.56

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GO1

2go1


Resolution: 2.233→42.772 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.82
RfactorNum. reflection% reflection
Rfree0.2221 1406 5.1 %
Rwork0.1866 --
obs0.1884 27556 74.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.233→42.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5798 0 6 201 6005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045949
X-RAY DIFFRACTIONf_angle_d0.8528109
X-RAY DIFFRACTIONf_dihedral_angle_d6.0743553
X-RAY DIFFRACTIONf_chiral_restr0.048908
X-RAY DIFFRACTIONf_plane_restr0.0061050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2326-2.31240.3218590.23191208X-RAY DIFFRACTION35
2.3124-2.4050.2946760.22181565X-RAY DIFFRACTION45
2.405-2.51440.26291080.23241819X-RAY DIFFRACTION52
2.5144-2.6470.28111110.22582146X-RAY DIFFRACTION62
2.647-2.81280.25661450.22032558X-RAY DIFFRACTION73
2.8128-3.02990.25111580.21262939X-RAY DIFFRACTION85
3.0299-3.33470.25531790.20163304X-RAY DIFFRACTION94
3.3347-3.8170.22961860.17773528X-RAY DIFFRACTION100
3.817-4.8080.16951810.15213492X-RAY DIFFRACTION99
4.808-42.77950.19572030.17743591X-RAY DIFFRACTION99

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