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

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Basic information

Entry
Database: PDB / ID: 6juj
TitleCrystal structure of Formate dehydrogenase mutant V198I/C256I/P260S/E261P/S381N/S383F from Pseudomonas sp. 101in complex with non-natural cofactor Nicotinamide Cytosine Dinucleotide
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 / 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
Chem-A7R / Formate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. 101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 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 14, 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)90,2689
Polymers88,5262
Non-polymers1,7417
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-41 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.026, 54.078, 117.909
Angle α, β, γ (deg.)90.00, 122.62, 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,P260S,E261P,S381N,S383F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. 101 (bacteria) / Strain: 101 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33160, formate dehydrogenase
#2: Chemical ChemComp-A7R / [[(2S,3S,4R,5S)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 640.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N5O15P2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
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: 2.18→50 Å / Num. obs: 36097 / % possible obs: 80.95 % / Redundancy: 2.6 % / Biso Wilson estimate: 29.94 Å2 / Rmerge(I) obs: 0.1082 / Net I/σ(I): 7.03
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.56 / Num. unique obs: 2461 / % possible all: 61.4

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Processing

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

2go1


Resolution: 2.183→49.657 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1664 5.06 %
Rwork0.1709 --
obs0.1733 32899 80.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.183→49.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 114 356 6360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086154
X-RAY DIFFRACTIONf_angle_d1.1758395
X-RAY DIFFRACTIONf_dihedral_angle_d6.6833618
X-RAY DIFFRACTIONf_chiral_restr0.067936
X-RAY DIFFRACTIONf_plane_restr0.0071075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1833-2.24750.2943880.21331940X-RAY DIFFRACTION61
2.2475-2.32010.30471060.20592085X-RAY DIFFRACTION66
2.3201-2.4030.27021380.20182217X-RAY DIFFRACTION70
2.403-2.49920.2711120.20192330X-RAY DIFFRACTION73
2.4992-2.6130.24241240.19232464X-RAY DIFFRACTION77
2.613-2.75070.24521540.19722648X-RAY DIFFRACTION83
2.7507-2.9230.23751510.19862809X-RAY DIFFRACTION88
2.923-3.14870.25951520.19862886X-RAY DIFFRACTION90
3.1487-3.46550.24621640.18242967X-RAY DIFFRACTION93
3.4655-3.96680.18581560.15532989X-RAY DIFFRACTION92
3.9668-4.99690.16191580.13022950X-RAY DIFFRACTION90
4.9969-49.67030.20021610.15572950X-RAY DIFFRACTION88

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