[English] 日本語
Yorodumi
- PDB-5c5u: The crystal structure of viral collagen prolyl hydroxylase vCPH f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c5u
TitleThe crystal structure of viral collagen prolyl hydroxylase vCPH from Paramecium Bursaria Chlorella virus-1 - Truncated Construct
ComponentsProlyl 4-hydroxylase
KeywordsHYDROLASE / 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
ACETATE ION / : / Prolyl 4-hydroxylase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLongbotham, J.E. / Levy, C.W. / Johannisen, L.O. / Tarhonskaya, H. / Jiang, S. / Loenarz, C. / Flashman, E. / Hay, S. / Schofiled, C.J. / Scrutton, N.S.
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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,90616
Polymers51,7372
Non-polymers16914
Water9,476526
1
A: Prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9238
Polymers25,8681
Non-polymers557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9828
Polymers25,8681
Non-polymers1147
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.770, 157.670, 41.010
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

-
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: vCPH was concentrated to 30 mg/ml in 100 mM HEPES, pH 7.5, before being supplemented with 1.1 mM MnCl2. Crystals of vCPH were grown by sitting drop vapour diffusion, incubated at 4 C and ...Details: vCPH was concentrated to 30 mg/ml in 100 mM HEPES, pH 7.5, before being supplemented with 1.1 mM MnCl2. Crystals of vCPH were grown by sitting drop vapour diffusion, incubated at 4 C and arose from a reservoir solution containing 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].

-
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: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→28.4 Å / Num. obs: 44328 / % possible obs: 94.56 % / Redundancy: 3.1 % / Net I/σ(I): 10.4

-
Processing

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

2jig


Resolution: 1.7→28.4 Å / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 28.94 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2024 2085 4.7 %
Rwork0.156 --
obs0.163 44328 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 17 526 3588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053126
X-RAY DIFFRACTIONf_angle_d0.8724208
X-RAY DIFFRACTIONf_dihedral_angle_d12.6981191
X-RAY DIFFRACTIONf_chiral_restr0.044435
X-RAY DIFFRACTIONf_plane_restr0.004538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7019-1.74440.26821240.22672392X-RAY DIFFRACTION73
1.7444-1.79160.23721390.21712929X-RAY DIFFRACTION86
1.7916-1.84430.23381450.19543089X-RAY DIFFRACTION93
1.8443-1.90380.23181470.18813111X-RAY DIFFRACTION94
1.9038-1.97180.23651570.17513177X-RAY DIFFRACTION94
1.9718-2.05070.20131450.17623034X-RAY DIFFRACTION92
2.0507-2.1440.22211370.16063004X-RAY DIFFRACTION90
2.144-2.2570.24521360.16612864X-RAY DIFFRACTION85
2.257-2.39830.22971380.15583045X-RAY DIFFRACTION91
2.3983-2.58330.21261500.15373068X-RAY DIFFRACTION93
2.5833-2.8430.1811400.15683154X-RAY DIFFRACTION94
2.843-3.25370.20231430.15243085X-RAY DIFFRACTION93
3.2537-4.09670.19091530.14633183X-RAY DIFFRACTION94
4.0967-25.72660.17881490.14033164X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.85371.30560.92932.90611.89652.51250.0508-0.4065-0.77480.58060.03-0.47750.50340.4201-0.28780.17770.0409-0.00520.19810.03630.251218.05459.082616.9886
20.83850.1412-0.0240.9004-0.20240.7340.0139-0.00230.0022-0.0006-0.009-0.01660.0092-0.0155-0.00480.03170.0158-0.00630.0638-0.00590.060140.085721.153617.1022
31.8181-0.7437-0.36860.9540.73950.60810.0514-0.07090.49330.0018-0.0501-0.0811-0.29690.0472-0.10740.1333-0.0086-0.03450.10.01320.1911.259868.9882-1.6982
41.5702-0.45330.24571.3504-0.36350.73310.04080.073-0.0357-0.0602-0.0447-0.02510.00360.01140.01020.0441-0.0091-0.00840.08920.00440.05827.479153.7931-6.9785
51.01440.1397-0.05840.706-0.16490.92060.0363-0.01690.05040.0633-0.02170.0164-0.0734-0.0053-0.01460.0261-0.0036-0.01270.07250.00720.079820.32159.49641.8174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 241 )
3X-RAY DIFFRACTION3chain 'B' and (resid 33 through 46 )
4X-RAY DIFFRACTION4chain 'B' and (resid 47 through 138 )
5X-RAY DIFFRACTION5chain 'B' and (resid 139 through 242 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more