[English] 日本語
Yorodumi
- PDB-1irm: Crystal structure of apo heme oxygenase-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1irm
TitleCrystal structure of apo heme oxygenase-1
Componentsapo heme oxygenase-1
KeywordsOXIDOREDUCTASE / disordered alpha helix / apo form of hemoprotein
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / arachidonate omega-hydroxylase 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 / cellular response to cisplatin ...Regulation of HMOX1 expression and activity / arachidonate omega-hydroxylase 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 / cellular response to cisplatin / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / phospholipase D activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / negative regulation of ferroptosis / epithelial cell apoptotic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / liver regeneration / macroautophagy / response to nicotine / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to hydrogen peroxide / caveola / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to heat / angiogenesis / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / response to oxidative stress / 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 / identical protein binding / nucleus / metal ion binding / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSugishima, M. / Sakamoto, H. / Kakuta, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystal structure of rat apo-heme oxygenase-1 (HO-1): mechanism of heme binding in HO-1 inferred from structural comparison of the apo and heme complex forms
Authors: Sugishima, M. / Sakamoto, H. / Kakuta, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K.
#1: Journal: FEBS Lett. / Year: 2000
Title: Crystal Structure of rat heme oxygenase-1 in complex with heme
Authors: Sugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray diffraction studies on the water soluble form of rat heme oxygenase-1 in complex with heme
Authors: Omata, Y. / Asada, S. / Sakamoto, H. / Fukuyama, K. / Noguchi, M.
History
DepositionOct 9, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2002Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: apo heme oxygenase-1
A: apo heme oxygenase-1
B: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)91,8373
Polymers91,8373
Non-polymers00
Water1,56787
1
C: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)30,6121
Polymers30,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)30,6121
Polymers30,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)30,6121
Polymers30,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.210, 70.210, 140.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein apo heme oxygenase-1 / HO-1


Mass: 30612.496 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, PEG400, HEPES, stronthium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 Mammonium sulfate1reservoir
22 %PEG4001reservoir
35 mM1reservoirSrCl2
40.1 MHEPES-NaOH1reservoirpH8.0
520 mg/mlprotein1drop
620 mMTris-HCl1droppH7.4
750 mM1dropKCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.709 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2000
RadiationMonochromator: Si(111) double monochrometor / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.709 Å / Relative weight: 1
ReflectionResolution: 2.55→46.625 Å / Num. all: 25283 / Num. obs: 25283 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3692 / Rsym value: 0.25 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 93875 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.25

-
Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DVE

1dve


Resolution: 2.55→46.625 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: To solve the structure of merohedral twinning crystal, LSQ refinement target used as ( Fo - k( sqrt 0.55Fc^2 + 0.45Fc'^2] ) )^2
RfactorNum. reflection% reflectionSelection details
Rfree0.3068 1110 4.6 %random but, the pairs of twin related reflections are in the same set
Rwork0.2024 ---
all0.204 24264 --
obs0.204 24264 96 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.294 Å2-8.294 Å216.588 Å2
2---7.906 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.55→46.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 0 87 4836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00876
X-RAY DIFFRACTIONc_angle_deg1.464
X-RAY DIFFRACTIONc_dihedral_angle_d22.26
X-RAY DIFFRACTIONc_improper_angle_d0.968
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.55-2.640.3853994.570.3222068499885.6
2.75-3.020.36262050.2815492094.8
3.02-3.460.32172250.2292500399.2
3.46-4.360.28392350.1687505099.9
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.968
LS refinement shell
*PLUS
Rfactor Rfree: 0.3853 / Rfactor Rwork: 0.322

+
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