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- PDB-6iuq: Crystal structure and expression patterns of prolyl 4-hydroxylase... -

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Basic information

Entry
Database: PDB / ID: 6iuq
TitleCrystal structure and expression patterns of prolyl 4-hydroxylases from Phytophthora capsici
ComponentsProlyl 4-hydroxylaseProcollagen-proline dioxygenase
KeywordsOXIDOREDUCTASE / hydroxylase / iron / DSBH core fold
Function / homology
Function and homology information


L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding
Similarity search - Function
2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / Prolyl 4-hydroxylase
Similarity search - Component
Biological speciesPhytophthora capsici LT1534 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.348 Å
AuthorsSong, W.W. / Zhang, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
CARS-25-03B China
CitationJournal: To Be Published
Title: Crystal structure and expression patterns of prolyl 4-hydroxylases from Phytophthora capsici
Authors: Song, W.W. / Zhang, X.G.
History
DepositionNov 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prolyl 4-hydroxylase
B: Prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0754
Polymers80,9632
Non-polymers1122
Water4,486249
1
A: Prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5372
Polymers40,4811
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area14360 Å2
MethodPISA
2
B: Prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5372
Polymers40,4811
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.724, 63.782, 72.845
Angle α, β, γ (deg.)80.18, 65.27, 71.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Prolyl 4-hydroxylase / Procollagen-proline dioxygenase


Mass: 40481.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: each monomer consisits of an iron ion
Source: (gene. exp.) Phytophthora capsici LT1534 (eukaryote)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYH8*PLUS
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGenBank number of this polypeptide is MH251252.

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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: 3.04 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate tribasic dehydrate pH5.0, 18% (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.348→50 Å / Num. obs: 38776 / % possible obs: 98 % / Redundancy: 5.3 % / Rpim(I) all: 0.029 / Net I/σ(I): 8.7
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 1882 / Rpim(I) all: 0.172

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.348→43.669 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 22.56
RfactorNum. reflection% reflection
Rfree0.2168 1861 5.04 %
Rwork0.1844 --
obs0.1861 36918 92.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.348→43.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4844 0 2 249 5095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084966
X-RAY DIFFRACTIONf_angle_d1.0986717
X-RAY DIFFRACTIONf_dihedral_angle_d15.5081849
X-RAY DIFFRACTIONf_chiral_restr0.042709
X-RAY DIFFRACTIONf_plane_restr0.006878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3482-2.41170.24621110.20592003X-RAY DIFFRACTION69
2.4117-2.48270.28231140.19572213X-RAY DIFFRACTION75
2.4827-2.56280.25131290.19322431X-RAY DIFFRACTION84
2.5628-2.65440.24311410.19832730X-RAY DIFFRACTION94
2.6544-2.76070.24241700.19352819X-RAY DIFFRACTION97
2.7607-2.88630.2011360.19482865X-RAY DIFFRACTION98
2.8863-3.03840.24821460.20712868X-RAY DIFFRACTION98
3.0384-3.22870.21511500.18942812X-RAY DIFFRACTION97
3.2287-3.47790.19671380.17512886X-RAY DIFFRACTION98
3.4779-3.82770.19351600.17112872X-RAY DIFFRACTION99
3.8277-4.38120.21741360.16452894X-RAY DIFFRACTION99
4.3812-5.51810.18211710.16242807X-RAY DIFFRACTION98
5.5181-6.370.23551590.2092857X-RAY DIFFRACTION98

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