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- PDB-6ih2: Crystal structure of Phosphite Dehydrogenase from Ralstonia sp. 4506 -

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Basic information

Entry
Database: PDB / ID: 6ih2
TitleCrystal structure of Phosphite Dehydrogenase from Ralstonia sp. 4506
ComponentsPhosphite dehydrogenase
KeywordsOXIDOREDUCTASE / Phosphite Dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
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 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 ...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
Phosphite dehydrogenase
Similarity search - Component
Biological speciesRalstonia sp. 4506 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.048 Å
AuthorsSong, X. / Zhao, Z. / Liu, Y. / Feng, Y.
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

Downloads & links

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Assembly

Deposited unit
A: Phosphite dehydrogenase
B: Phosphite dehydrogenase


Theoretical massNumber of molelcules
Total (without water)73,2552
Polymers73,2552
Non-polymers00
Water10,215567
1
A: Phosphite dehydrogenase

B: Phosphite dehydrogenase


Theoretical massNumber of molelcules
Total (without water)73,2552
Polymers73,2552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y+1/2,-z+5/21
Buried area6120 Å2
ΔGint-35 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.653, 97.849, 122.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Phosphite dehydrogenase


Mass: 36627.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. 4506 (bacteria) / Gene: ptxD / Production host: Escherichia coli (E. coli) / References: UniProt: G4XDR8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8
Details: 0.2 M NaCl, 0.1 M Tris-HCl pH 8.0, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.048→38.324 Å / Num. obs: 46894 / % possible obs: 98.79 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.46 / Num. unique obs: 4180 / % possible all: 89.79

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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: 2.048→38.324 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 2319 4.95 %
Rwork0.1624 --
obs0.164 46825 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.048→38.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 0 567 5601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075132
X-RAY DIFFRACTIONf_angle_d0.8526976
X-RAY DIFFRACTIONf_dihedral_angle_d2.7973120
X-RAY DIFFRACTIONf_chiral_restr0.052816
X-RAY DIFFRACTIONf_plane_restr0.005898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.048-2.08980.2341090.16762147X-RAY DIFFRACTION83
2.0898-2.13520.21111210.16552649X-RAY DIFFRACTION100
2.1352-2.18490.21251050.16642605X-RAY DIFFRACTION99
2.1849-2.23950.21171500.16752595X-RAY DIFFRACTION100
2.2395-2.30010.2061420.16272595X-RAY DIFFRACTION100
2.3001-2.36780.20411540.16132609X-RAY DIFFRACTION100
2.3678-2.44420.18741420.16562614X-RAY DIFFRACTION100
2.4442-2.53150.24631410.16552614X-RAY DIFFRACTION100
2.5315-2.63280.21411360.17172643X-RAY DIFFRACTION100
2.6328-2.75260.22831300.17372629X-RAY DIFFRACTION100
2.7526-2.89770.20731290.17332643X-RAY DIFFRACTION100
2.8977-3.07920.20691360.17522654X-RAY DIFFRACTION100
3.0792-3.31680.20571420.16912642X-RAY DIFFRACTION100
3.3168-3.65040.20651460.16042656X-RAY DIFFRACTION100
3.6504-4.1780.1711380.1452674X-RAY DIFFRACTION100
4.178-5.26170.17741470.14292723X-RAY DIFFRACTION100
5.2617-38.33070.14711510.17252814X-RAY DIFFRACTION99

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