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- PDB-6jwg: Crystal structure of Formate dehydrogenase mutant C256I/E261P/S38... -

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Basic information

Entry
Database: PDB / ID: 6jwg
TitleCrystal structure of Formate dehydrogenase mutant C256I/E261P/S381I 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: 2.081 Å
AuthorsFeng, Y. / Guo, X. / Xue, S. / 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 20, 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)88,7035
Polymers88,3962
Non-polymers3063
Water12,340685
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-36 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.186, 95.792, 112.458
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-949-

HOH

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Components

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


Mass: 44198.184 Da / Num. of mol.: 2 / Mutation: C256I/E261P/S381I
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5,000

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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: 2.08→50 Å / Num. obs: 53181 / % possible obs: 95.98 % / Redundancy: 5.6 % / Biso Wilson estimate: 25.03 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.86
Reflection shellResolution: 2.08→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.86 / Num. unique obs: 3759 / CC1/2: 0.881 / % possible all: 68.53

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GO1

2go1


Resolution: 2.081→44.062 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.96
RfactorNum. reflection% reflection
Rfree0.1873 2006 3.77 %
Rwork0.1692 --
obs0.1699 53151 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.081→44.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 20 685 6519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045981
X-RAY DIFFRACTIONf_angle_d0.88156
X-RAY DIFFRACTIONf_dihedral_angle_d4.7633571
X-RAY DIFFRACTIONf_chiral_restr0.049910
X-RAY DIFFRACTIONf_plane_restr0.0051057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0815-2.13350.2563800.23012332X-RAY DIFFRACTION62
2.1335-2.19120.22811370.21033325X-RAY DIFFRACTION88
2.1912-2.25570.21661520.19843717X-RAY DIFFRACTION98
2.2557-2.32850.23581390.19183772X-RAY DIFFRACTION99
2.3285-2.41170.22291610.1953768X-RAY DIFFRACTION100
2.4117-2.50830.22071370.1873787X-RAY DIFFRACTION100
2.5083-2.62240.18291570.1793772X-RAY DIFFRACTION100
2.6224-2.76060.20741460.17743757X-RAY DIFFRACTION100
2.7606-2.93360.17931450.18543844X-RAY DIFFRACTION100
2.9336-3.160.22151500.18043758X-RAY DIFFRACTION100
3.16-3.47790.20811470.17563827X-RAY DIFFRACTION100
3.4779-3.98090.14721520.153810X-RAY DIFFRACTION100
3.9809-5.01430.13981460.12863837X-RAY DIFFRACTION100
5.0143-44.07210.17881570.1593839X-RAY DIFFRACTION99

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