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- PDB-6ih8: Crystal structure of Phosphite Dehydrogenase mutant I151R/P176R/M... -

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Basic information

Entry
Database: PDB / ID: 6ih8
TitleCrystal structure of Phosphite Dehydrogenase mutant I151R/P176R/M207A 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: 2.25 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
C: Phosphite dehydrogenase
D: Phosphite dehydrogenase


Theoretical massNumber of molelcules
Total (without water)147,6554
Polymers147,6554
Non-polymers00
Water11,133618
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-49 kcal/mol
Surface area55280 Å2
2
A: Phosphite dehydrogenase
D: Phosphite dehydrogenase


Theoretical massNumber of molelcules
Total (without water)73,8272
Polymers73,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-37 kcal/mol
Surface area26660 Å2
MethodPISA
3
B: Phosphite dehydrogenase

C: Phosphite dehydrogenase


Theoretical massNumber of molelcules
Total (without water)73,8272
Polymers73,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area6150 Å2
ΔGint-34 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.030, 118.591, 98.228
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphite dehydrogenase


Mass: 36913.699 Da / Num. of mol.: 4 / Mutation: I151R, P176R,M207A
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.: 618 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
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: BL17U / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.25→26.75 Å / Num. obs: 67160 / % possible obs: 98.99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.8
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 6292

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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: 4E5M

4e5m


Resolution: 2.25→26.749 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.2135 3261 4.86 %
Rwork0.1764 --
obs0.1782 67147 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→26.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10084 0 0 618 10702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810279
X-RAY DIFFRACTIONf_angle_d0.88613966
X-RAY DIFFRACTIONf_dihedral_angle_d3.1656238
X-RAY DIFFRACTIONf_chiral_restr0.0531624
X-RAY DIFFRACTIONf_plane_restr0.0061800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2452-2.27870.26431190.25162518X-RAY DIFFRACTION89
2.2787-2.31420.30831530.23322671X-RAY DIFFRACTION96
2.3142-2.35220.22731120.21332752X-RAY DIFFRACTION98
2.3522-2.39270.30841310.21352800X-RAY DIFFRACTION99
2.3927-2.43620.27521350.21142754X-RAY DIFFRACTION99
2.4362-2.4830.24331490.21572811X-RAY DIFFRACTION99
2.483-2.53360.28841610.21622714X-RAY DIFFRACTION100
2.5336-2.58870.24731510.20782811X-RAY DIFFRACTION100
2.5887-2.64890.28141330.19922781X-RAY DIFFRACTION100
2.6489-2.7150.25981500.1972805X-RAY DIFFRACTION100
2.715-2.78840.27841400.19182779X-RAY DIFFRACTION100
2.7884-2.87030.2271670.19542780X-RAY DIFFRACTION100
2.8703-2.96290.22581450.19352822X-RAY DIFFRACTION100
2.9629-3.06860.25571250.19982800X-RAY DIFFRACTION100
3.0686-3.19130.21791350.18932779X-RAY DIFFRACTION100
3.1913-3.33630.24661480.18252797X-RAY DIFFRACTION100
3.3363-3.51180.20311360.18162813X-RAY DIFFRACTION100
3.5118-3.73130.20271340.16382810X-RAY DIFFRACTION100
3.7313-4.01850.19841490.1532788X-RAY DIFFRACTION100
4.0185-4.42130.14931500.13912824X-RAY DIFFRACTION100
4.4213-5.05730.15631280.13412818X-RAY DIFFRACTION100
5.0573-6.35750.19981470.17122836X-RAY DIFFRACTION100
6.3575-26.7510.15821630.14862823X-RAY DIFFRACTION99

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