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- PDB-5c5t: The crystal structure of viral collagen prolyl hydroxylase vCPH f... -

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Basic information

Entry
Database: PDB / ID: 5c5t
TitleThe crystal structure of viral collagen prolyl hydroxylase vCPH from Paramecium Bursaria Chlorella virus-1 - 2OG complex
ComponentsProlyl 4-hydroxylase
KeywordsOXIDOREDUCTASE / dioxygenase / prolyl hydroxylase
Function / homology
Function and homology information


L-ascorbic acid binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / dioxygenase activity / iron ion binding / membrane
Similarity search - Function
Prolyl 4-hydroxylase / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls ...Prolyl 4-hydroxylase / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Prolyl 4-hydroxylase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Biochemistry / Year: 2015
Title: Structure and Mechanism of a Viral Collagen Prolyl Hydroxylase.
Authors: Longbotham, J.E. / Levy, C. / Johannissen, L.O. / Tarhonskaya, H. / Jiang, S. / Loenarz, C. / Flashman, E. / Hay, S. / Schofield, C.J. / Scrutton, N.S.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,2157
Polymers51,7372
Non-polymers4785
Water7,134396
1
A: Prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1354
Polymers25,8681
Non-polymers2663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0803
Polymers25,8681
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.790, 156.950, 41.240
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Prolyl 4-hydroxylase


Mass: 25868.334 Da / Num. of mol.: 2 / Fragment: residues 36-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Gene: A085R / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q84406
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M [Imidazole; MES monohydrate (acid)], 0.1 M amino acids [0.2 M L-Na-Glutamate; 0.2 M Alanine (racemic); 0.2 M Glycine; 0.2M Lysine HCL (racemic); 0.2 M Serine (racemic)], 30 % PEGMME ...Details: 0.1 M [Imidazole; MES monohydrate (acid)], 0.1 M amino acids [0.2 M L-Na-Glutamate; 0.2 M Alanine (racemic); 0.2 M Glycine; 0.2M Lysine HCL (racemic); 0.2 M Serine (racemic)], 30 % PEGMME 550 PEG 20K pH 6.5 [Morpheus HT96 condition H1, Molecular Dimensions] COmplex generated by soaking crystals in mother liquor supplemented with 250 mM ZnSO4 and 100 mM 2-OG for a period of 16 hours.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.598→28.43 Å / Num. obs: 55206 / % possible obs: 98 % / Redundancy: 3.4 % / Net I/σ(I): 13.55

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Processing

Software
NameVersionClassification
PHENIXdev_1977refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JIG

2jig


Resolution: 1.598→28.427 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1978 3.58 %Random
Rwork0.1775 ---
obs0.1787 55202 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.598→28.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 23 396 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163008
X-RAY DIFFRACTIONf_angle_d1.4834055
X-RAY DIFFRACTIONf_dihedral_angle_d15.6321156
X-RAY DIFFRACTIONf_chiral_restr0.076418
X-RAY DIFFRACTIONf_plane_restr0.008516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5983-1.63820.27851360.24113596X-RAY DIFFRACTION93
1.6382-1.68250.25811440.22243860X-RAY DIFFRACTION99
1.6825-1.7320.25671400.20853788X-RAY DIFFRACTION98
1.732-1.78790.26271390.19723782X-RAY DIFFRACTION96
1.7879-1.85180.23971410.18523800X-RAY DIFFRACTION99
1.8518-1.9260.22771420.18523823X-RAY DIFFRACTION99
1.926-2.01360.19091420.1733859X-RAY DIFFRACTION99
2.0136-2.11970.21271450.1653861X-RAY DIFFRACTION99
2.1197-2.25250.21071440.16423877X-RAY DIFFRACTION99
2.2525-2.42630.19121420.17053804X-RAY DIFFRACTION97
2.4263-2.67030.24151440.17273745X-RAY DIFFRACTION97
2.6703-3.05630.211430.17953825X-RAY DIFFRACTION98
3.0563-3.84910.21641300.17023804X-RAY DIFFRACTION97
3.8491-28.43120.17241460.17333800X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -2.4289 Å / Origin y: 37.0732 Å / Origin z: -13.2288 Å
111213212223313233
T0.0911 Å20.0183 Å2-0.0076 Å2-0.116 Å20.0047 Å2--0.0944 Å2
L0.4798 °20.4914 °2-0.272 °2-1.0257 °2-0.4654 °2--0.4862 °2
S0.0074 Å °0.0153 Å °-0.0034 Å °-0.0077 Å °-0.0006 Å °-0.0045 Å °0.0026 Å °0.0112 Å °-0.0048 Å °
Refinement TLS groupSelection details: all

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