[English] 日本語
Yorodumi
- PDB-1prh: THE X-RAY CRYSTAL STRUCTURE OF THE MEMBRANE PROTEIN PROSTAGLANDIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1prh
TitleTHE X-RAY CRYSTAL STRUCTURE OF THE MEMBRANE PROTEIN PROSTAGLANDIN H2 SYNTHASE-1
ComponentsPROSTAGLANDIN H2 SYNTHASE-1
KeywordsOXIDOREDUCTASE(DIOXYGENASE / PEROXIDASE)
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain ...: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsPicot, D. / Loll, P.J. / Garavito, R.M.
Citation
Journal: Nature / Year: 1994
Title: The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1.
Authors: Picot, D. / Loll, P.J. / Garavito, R.M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: X-Ray Crystal Structure of Canine Myeloperoxidase at 3 Angstroms Resolution
Authors: Zeng, J. / Fenna, R.E.
History
DepositionMar 7, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650HELIX HELIX -- THE NOMENCLATURE FOR THE HELICES 1 - 19 IS BASED ON THE TOPOLOGICAL AND SPATIAL ...HELIX HELIX -- THE NOMENCLATURE FOR THE HELICES 1 - 19 IS BASED ON THE TOPOLOGICAL AND SPATIAL EQUIVALENCE OF SECONDARY STRUCTURE BETWEEN PROSTAGLANDIN H SYNTHASE AND MYELO-PEROXIDASE (ZENG AND FENNA, 1992). HELICES IDENTIFIED WITH A LETTER A - E HAVE NO EQUIVALENT IN MYELOPEROXIDASE.
Remark 700SHEET SHEET -- ONLY A SMALL REGION OF BETA-SHEET IS OBSERVED IN THE EGF-LIKE MODULE (RESIDUES 33 - ...SHEET SHEET -- ONLY A SMALL REGION OF BETA-SHEET IS OBSERVED IN THE EGF-LIKE MODULE (RESIDUES 33 - 72) ALTHOUGH THE EXACT HYDROGEN BONDING SCHEME IS NOT UNEQUIVOCAL AT THE PRESENT RESOLUTION.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROSTAGLANDIN H2 SYNTHASE-1
B: PROSTAGLANDIN H2 SYNTHASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9684
Polymers127,7352
Non-polymers1,2332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-66 kcal/mol
Surface area41010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.400, 210.300, 233.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO A 127
2: ASP A 584 - PRO A 585 OMEGA = 240.54 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO B 127
4: ASP B 584 - PRO B 585 OMEGA = 240.42 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99534, -0.0599, 0.07562), (-0.05926, -0.23888, -0.96924), (0.07612, -0.9692, 0.23422)
Vector: 81.43, 234.505, 179.08299)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

-
Components

#1: Protein PROSTAGLANDIN H2 SYNTHASE-1


Mass: 63867.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep)
References: UniProt: P05979, prostaglandin-endoperoxide synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Compound detailsRESIDUES ASN 68, ASN 144 AND ASN 410 ARE GLYCOSYLATED AND THE FIRST 1 - 2 SUGARS ARE VISIBLE IN THE MAP(S).
Has protein modificationY
Nonpolymer detailsCOX -- THE CYCLOOXYGENASE ACTIVE SITE IS LOCATED WITHIN A LONG HYDROPHOBIC CHANNEL AT A REGION ...COX -- THE CYCLOOXYGENASE ACTIVE SITE IS LOCATED WITHIN A LONG HYDROPHOBIC CHANNEL AT A REGION DEFINED BY RESIDUES ARG 120, SER 530 (SITE OF ASPIRIN ACETYLATION), TYR 385, AND GLU 524. THE CRYSTALS CONTAIN A NON-STEROIDAL ANTI-INFLAMMATORY DRUG FLURBIPROFEN AND THE DRUG BINDING SITE HAS BEEN IDENTIFIED (SEE D. PICOT, P.J. LOLL AND R.M. GARAVITO, 1994), ALTHOUGH REGULARIZED AND REFINED COORDINATES FOR THE PROTEIN-BOUND DRUG ARE NOT YET AVAILABLE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.77 Å3/Da / Density % sol: 74.19 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mMsodium phosphate1drop
2100-200 mM1dropNaCl
30.6 %(w/v)beta-octyl glucopyranoside1drop
40.1 mMflurbiprofen1drop
52-4 %PEG40001drop
620 mMsodium phosphate1reservoir2-4 times concentrate
7100-200 mM1reservoirNaCl2-4 times concentrate
80.6 %(w/v)beta-octyl glucopyranoside1reservoir2-4 times concentrate
90.1 mMflurbiprofen1reservoir2-4 times concentrate
104-8 %PEG40001reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.4 Å / Num. obs: 32349 / % possible obs: 96.3 % / Num. measured all: 112745 / Rmerge(I) obs: 0.076

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→20 Å / σ(F): 2
Details: COORDINATES GIVEN HERE FOR RESIDUES 33 - 586 WHERE THE MAIN CHAIN ELECTRON DENSITY IS WELL DEFINED. ELECTRON DENSITY FOR THE EXTREME AMINO-TERMINUS (RESIDUES 25 - 33) AND THE EXTREME C- ...Details: COORDINATES GIVEN HERE FOR RESIDUES 33 - 586 WHERE THE MAIN CHAIN ELECTRON DENSITY IS WELL DEFINED. ELECTRON DENSITY FOR THE EXTREME AMINO-TERMINUS (RESIDUES 25 - 33) AND THE EXTREME C-TERMINUS (RESIDUES 587 - 600) IS POORLY DEFINED. RESOLUTION IS TOO LIMITED TO CLEARLY DEFINE TURN STEREOCHEMISTRY. PHASED BY MIR (3 DERIVATIVES), SOLVENT FLATTENED AND TWO-FOLD AVERAGED ABOUT THE NON-CRYSTALLOGRAPHIC SYMMETRY AXIS.
RfactorNum. reflection
Rfree0.316 -
Rwork0.267 -
obs0.267 32349
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 86 0 9092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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://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