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- PDB-1ix4: Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bo... -

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Basic information

Entry
Database: PDB / ID: 1ix4
TitleCrystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide
ComponentsHEME OXYGENASE-1Heme oxygenase
KeywordsOXIDOREDUCTASE / HEMEPROTEIN / INHIBITOR COMPLEX
Function / homology
Function and homology information


response to 3-methylcholanthrene / Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / heme metabolic process / response to arachidonic acid / phospholipase D activity ...response to 3-methylcholanthrene / Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / heme metabolic process / response to arachidonic acid / phospholipase D activity / heme oxygenase (biliverdin-producing) / cellular response to cisplatin / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) 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 nutrient / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / erythrocyte homeostasis / epithelial cell apoptotic process / positive regulation of epithelial cell apoptotic process / negative regulation of macroautophagy / small GTPase-mediated signal transduction / positive regulation of cell migration involved in sprouting angiogenesis / 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 / response to nicotine / liver regeneration / caveola / negative regulation of smooth muscle cell proliferation / macroautophagy / positive regulation of smooth muscle cell proliferation / response to hydrogen peroxide / 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 / cellular response to hypoxia / angiogenesis / response to oxidative stress / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / structural molecule activity / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / metal ion binding / nucleus
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSugishima, M. / Sakamoto, H. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal Structures of Ferrous and CO-, CN(-)-, and NO-Bound Forms of Rat Heme Oxygenase-1 (HO-1) in Complex with Heme: Structural Implications for Discrimination between CO and O(2) in HO-1.
Authors: Sugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of rat heme oxygenase-1 in complex with heme bound to azide. Implication for regiospecific hydroxylation of heme at the alpha-meso carbon.
Authors: Sugishima, M. / Sakamoto, H. / Higashimoto, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K.
History
DepositionJun 10, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEME OXYGENASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2573
Polymers30,6121
Non-polymers6442
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.000, 66.000, 120.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 30612.496 Da / Num. of mol.: 1
Fragment: soluble fragment truncated C-terminal transmembrane helix
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pUC18 / 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, sodium azide, potassium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Sugishima, M., (2002) J.Biol.Chem., 277, 45086.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 Msodium formate1reservoir
218 mg/mlprotein1drop
350 mMpotassium phosphate1droppH7.0
45 mMsodium azide1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 29, 2002
RadiationMonochromator: Si(111) double-monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 28941 / Num. obs: 28311 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rsym value: 0.067 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.86 Å / Num. unique all: 2592 / Rsym value: 0.311 / % possible all: 91.2
Reflection
*PLUS
Num. obs: 28853 / % possible obs: 99.7 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.315

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY

Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2813 -random
Rwork0.195 ---
obs0.197 25369 88.1 %-
all-28182 --
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 45 176 1932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.24
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d18.56
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.247 245 -
Rwork0.227 --
obs-2633 93.8 %
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.56
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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