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- PDB-6ih6: Phosphite Dehydrogenase mutant I151R/P176R/M207A from Ralstonia s... -

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Basic information

Entry
Database: PDB / ID: 6ih6
TitlePhosphite Dehydrogenase mutant I151R/P176R/M207A from Ralstonia sp. 4506 in complex with non-natural cofactor Nicotinamide Cytosine dinucleotide
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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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 / Phosphite dehydrogenase
Similarity search - Component
Biological speciesRalstonia sp. 4506 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.491 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Phosphite dehydrogenase
D: Phosphite dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9366
Polymers147,6554
Non-polymers1,2812
Water3,837213
1
A: Phosphite dehydrogenase
hetero molecules

D: Phosphite dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,4683
Polymers73,8272
Non-polymers6401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area6110 Å2
ΔGint-35 kcal/mol
Surface area26420 Å2
MethodPISA
2
B: Phosphite dehydrogenase
C: Phosphite dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4683
Polymers73,8272
Non-polymers6401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-33 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.197, 118.872, 98.340
Angle α, β, γ (deg.)90.00, 90.31, 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: 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
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) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 48679 / % possible obs: 97.26 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.8
Reflection shellResolution: 2.49→2.53 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 6292 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.491→38.672 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 2441 5.02 %
Rwork0.1993 --
obs0.2022 48644 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.491→38.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10132 0 84 213 10429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110418
X-RAY DIFFRACTIONf_angle_d1.1814168
X-RAY DIFFRACTIONf_dihedral_angle_d17.0236284
X-RAY DIFFRACTIONf_chiral_restr0.0581648
X-RAY DIFFRACTIONf_plane_restr0.0071814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.491-2.54190.39311150.27362676X-RAY DIFFRACTION97
2.5419-2.59710.34021320.26992716X-RAY DIFFRACTION96
2.5971-2.65750.32021240.25832700X-RAY DIFFRACTION98
2.6575-2.7240.30951190.25052736X-RAY DIFFRACTION96
2.724-2.79760.33381540.25052684X-RAY DIFFRACTION97
2.7976-2.87990.31621480.25162656X-RAY DIFFRACTION96
2.8799-2.97280.29361760.23482687X-RAY DIFFRACTION96
2.9728-3.0790.32241630.22382625X-RAY DIFFRACTION96
3.079-3.20220.27641410.21832668X-RAY DIFFRACTION96
3.2022-3.34790.28041270.21252686X-RAY DIFFRACTION96
3.3479-3.52430.25931470.21122697X-RAY DIFFRACTION96
3.5243-3.74490.26491390.19672703X-RAY DIFFRACTION97
3.7449-4.03380.22021580.18312747X-RAY DIFFRACTION99
4.0338-4.43920.20621250.16482806X-RAY DIFFRACTION99
4.4392-5.08030.22051560.16512766X-RAY DIFFRACTION100
5.0803-6.3960.29091650.2012818X-RAY DIFFRACTION100
6.396-38.67680.17861520.16342832X-RAY DIFFRACTION99

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