[English] 日本語
Yorodumi
- PDB-3b98: Crystal structure of zebrafish prostacyclin synthase (cytochrome ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b98
TitleCrystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1)
ComponentsProstaglandin I2 synthase
KeywordsISOMERASE / prostacyclin synthase / cytochrome p450 8A1 / CYP8A1
Function / homology
Function and homology information


: / Eicosanoids / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-I synthase / prostaglandin-I synthase activity / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / prostaglandin biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity ...: / Eicosanoids / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-I synthase / prostaglandin-I synthase activity / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / prostaglandin biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Prostacyclin synthase / Prostacyclin synthase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLi, Y.-C. / Chiang, C.-W. / Yeh, H.-C. / Hsu, P.-Y. / Whitby, F.G. / Wang, L.-H. / Chan, N.-L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of Prostacyclin Synthase and Its Complexes with Substrate Analog and Inhibitor Reveal a Ligand-specific Heme Conformation Change
Authors: Li, Y.-C. / Chiang, C.-W. / Yeh, H.-C. / Hsu, P.-Y. / Whitby, F.G. / Wang, L.-H. / Chan, N.-L.
History
DepositionNov 3, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prostaglandin I2 synthase
B: Prostaglandin I2 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9314
Polymers109,6982
Non-polymers1,2332
Water5,080282
1
A: Prostaglandin I2 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4652
Polymers54,8491
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prostaglandin I2 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4652
Polymers54,8491
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.667, 87.896, 190.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Prostaglandin I2 synthase / cytochrome P450 8A1 / prostacyclin synthase


Mass: 54848.930 Da / Num. of mol.: 2 / Fragment: UNP residues 17-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pgis / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: A9LLA5, UniProt: F1RE08*PLUS, prostaglandin-I synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 microliter of concentrated protein solution (20mg/ml) in gel filtration buffer (20mM Tris-HCl pH 8.0, 150mM NaCl and 5mM beta-mercaptoethanol) was mixed with equal amount of reservoir ...Details: 1 microliter of concentrated protein solution (20mg/ml) in gel filtration buffer (20mM Tris-HCl pH 8.0, 150mM NaCl and 5mM beta-mercaptoethanol) was mixed with equal amount of reservoir solution (20% PEG 3350 plus either 50mM Tris-HCl (pH 8.0) or 50mM HEPES (Na-salt; pH 7.5)) and equilibrated against 450 microliter of reservoir solution at 277 K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2006 / Details: Toroidal FM
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. all: 60147 / Num. obs: 60087 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rsym value: 0.046 / Net I/σ(I): 18
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 5912 / Rsym value: 0.21 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IAG

2iag


Resolution: 2.08→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.904 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.254 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26414 3031 5.1 %RANDOM
Rwork0.22735 ---
all0.22921 60147 --
obs0.229 56980 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.442 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7075 0 86 282 7443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227334
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9969934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33323.314350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.895151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4951564
X-RAY DIFFRACTIONr_chiral_restr0.0730.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025562
X-RAY DIFFRACTIONr_nbd_refined0.1860.23379
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2386
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.256
X-RAY DIFFRACTIONr_mcbond_it1.53324509
X-RAY DIFFRACTIONr_mcangle_it2.37537012
X-RAY DIFFRACTIONr_scbond_it1.6923260
X-RAY DIFFRACTIONr_scangle_it2.4832918
LS refinement shellResolution: 2.081→2.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 221 -
Rwork0.224 4091 -
obs-5912 99.1 %

+
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