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- PDB-1ix3: Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bo... -

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Basic information

Entry
Database: PDB / ID: 1ix3
TitleCrystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Cyanide
ComponentsHEME OXYGENASE-1
KeywordsOXIDOREDUCTASE / HEMEPROTEIN / INHIBITOR COMPLEX / CO-ANALOG COMPLEX
Function / homology
Function and homology information


arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / Heme degradation / negative regulation of muscle cell apoptotic process / response to 3-methylcholanthrene / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process ...arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / Heme degradation / negative regulation of muscle cell apoptotic process / response to 3-methylcholanthrene / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 viral life cycle / negative regulation of mast cell cytokine production / positive regulation of epithelial cell apoptotic process / phospholipase D activity / positive regulation of cell migration involved in sprouting angiogenesis / epithelial cell apoptotic process / erythrocyte homeostasis / negative regulation of ferroptosis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / cellular response to cadmium ion / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / host-mediated suppression of viral transcription / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / phospholipid metabolic process / liver regeneration / positive regulation of smooth muscle cell proliferation / response to nicotine / macroautophagy / negative regulation of smooth muscle cell proliferation / response to hydrogen peroxide / caveola / multicellular organismal-level iron ion homeostasis / regulation of blood pressure / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to heat / response to oxidative stress / angiogenesis / 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 / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEME OXYGENASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2553
Polymers30,6121
Non-polymers6432
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.700, 65.700, 119.700
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 / 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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.69 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, potassium cyanide, potassium phosphate, 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: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 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: 2→28.8 Å / Num. all: 20634 / Num. obs: 20634 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.066 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2965 / Rsym value: 0.284 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 20629 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.284

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Processing

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

1ivj


Resolution: 2→28.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 965 -RANDOM
Rwork0.199 ---
obs0.203 18899 90.7 %-
all-19864 --
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 45 140 1983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.19
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d18.75
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.251 95 -
Rwork0.235 --
obs-1749 90.1 %
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.75
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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