[English] 日本語
Yorodumi
- PDB-1vgi: Crystal structure of xenon bound rat heme-heme oxygenase-1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vgi
TitleCrystal structure of xenon bound rat heme-heme oxygenase-1 complex
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / hydrophobic cavity / xenon binding
Function / homology
Function and homology information


arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / heme oxygenase (biliverdin-producing) ...arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / negative regulation of muscle cell apoptotic process / wound healing involved in inflammatory response / cellular response to cisplatin / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / heme catabolic process / negative regulation of mast cell cytokine production / positive regulation of epithelial cell apoptotic process / phospholipase D activity / epithelial cell apoptotic process / negative regulation of ferroptosis / erythrocyte homeostasis / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of macroautophagy / small GTPase-mediated signal transduction / cellular response to cadmium ion / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / phospholipid metabolic process / liver regeneration / response to nicotine / positive regulation of smooth muscle cell proliferation / macroautophagy / negative regulation of smooth muscle cell proliferation / caveola / response to hydrogen peroxide / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / cellular response to heat / angiogenesis / negative regulation of neuron apoptotic process / response to oxidative stress / intracellular iron ion homeostasis / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / XENON / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsSugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: CO-trapping site in heme oxygenase revealed by photolysis of its co-bound heme complex: mechanism of escaping from product inhibition
Authors: Sugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
History
DepositionApr 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4064
Polymers30,6121
Non-polymers7943
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.100, 65.100, 120.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Heme oxygenase 1 / HO-1 / HSP32


Mass: 30612.496 Da / Num. of mol.: 1 / Fragment: residues 1-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pBAce / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P06762, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Apr 11, 2004
RadiationMonochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24007 / Num. obs: 24007 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 31.155 Å2 / Rsym value: 0.042 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3433 / Rsym value: 0.321 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1ULX

1ulx


Resolution: 1.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1189 -RANDOM
Rwork0.201 ---
all0.202 23959 --
obs0.202 23702 98.9 %-
Displacement parametersBiso mean: 0.038 Å2
Baniso -1Baniso -2Baniso -3
1--3.682 Å2-3.682 Å27.365 Å2
2---3.291 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 46 70 1835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d19.03
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.334 131 -
Rwork0.274 --
obs-2266 96.7 %

+
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