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- PDB-6ih4: Crystal structure of Phosphite Dehydrogenase mutant I151R/P176E f... -

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Basic information

Entry
Database: PDB / ID: 6ih4
TitleCrystal structure of Phosphite Dehydrogenase mutant I151R/P176E from Ralstonia sp. 4506
ComponentsPhosphite dehydrogenase
KeywordsOXIDOREDUCTASE / Phosphite Dehydrogenase
Function / homology
Function and homology information


hydroxypyruvate reductase (NADH) activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol
Similarity search - Function
: / 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 ...: / 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
Phosphite dehydrogenase
Similarity search - Component
Biological speciesRalstonia sp. 4506 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSong, X. / Feng, Y. / Liu, Y. / Zhao, Z.
CitationJournal: Acs Catalysis / Year: 2019
Title: Structural Insights into Phosphite Dehydrogenase Variants Favoring a Non-natural Redox Cofactor
Authors: Liu, Y. / Feng, Y. / Wang, L. / Guo, X. / Liu, W. / Li, Q. / Wang, X. / Xue, S. / Zhao, Z.
History
DepositionSep 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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: Phosphite dehydrogenase
B: Phosphite dehydrogenase


Theoretical massNumber of molelcules
Total (without water)73,8912
Polymers73,8912
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-7 kcal/mol
Surface area29760 Å2
Unit cell
Length a, b, c (Å)60.560, 97.822, 61.640
Angle α, β, γ (deg.)90.00, 102.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphite dehydrogenase


Mass: 36945.738 Da / Num. of mol.: 2 / Mutation: I151R, P176E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. 4506 (bacteria) / Gene: ptxD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G4XDR8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M NaCl, 0.1 M Tris-HCl pH 8.0, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→30.06 Å / Num. obs: 21013 / % possible obs: 97.06 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 9.98
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 1767

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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: 4E5M

4e5m


Resolution: 2.6→30 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.95
RfactorNum. reflection% reflection
Rfree0.2221 1032 4.91 %
Rwork0.1761 --
obs0.1782 21002 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 0 159 5195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035132
X-RAY DIFFRACTIONf_angle_d0.586972
X-RAY DIFFRACTIONf_dihedral_angle_d2.7653120
X-RAY DIFFRACTIONf_chiral_restr0.041813
X-RAY DIFFRACTIONf_plane_restr0.004899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.73810.32891290.22472513X-RAY DIFFRACTION85
2.7381-2.90960.28421560.21022821X-RAY DIFFRACTION97
2.9096-3.13410.21451300.20152926X-RAY DIFFRACTION100
3.1341-3.44930.23921540.19032905X-RAY DIFFRACTION99
3.4493-3.94790.21491590.1582916X-RAY DIFFRACTION100
3.9479-4.97170.16751680.14932906X-RAY DIFFRACTION99
4.9717-35.52650.23241360.17092983X-RAY DIFFRACTION99

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