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- PDB-1j2c: Crystal structure of rat heme oxygenase-1 in complex with biliver... -

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Basic information

Entry
Database: PDB / ID: 1j2c
TitleCrystal structure of rat heme oxygenase-1 in complex with biliverdin IXalpha-iron cluster
ComponentsHeme Oxygenase-1
KeywordsOXIDOREDUCTASE / ENZYME-PRODUCT complex / BENT HELIX
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 / epithelial cell apoptotic process / positive regulation of cell migration involved in sprouting angiogenesis / 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
BILIVERDINE IX ALPHA / : / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Rat Heme Oxygenase-1 in Complex with Biliverdin-Iron Chelate: CONFORMATIONAL CHANGE OF THE DISTAL HELIX DURING THE HEME CLEAVAGE REACTION.
Authors: Sugishima, M. / Sakamoto, H. / Higashimoto, Y. / Noguchi, M. / Fukuyama, K.
History
DepositionDec 29, 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

Downloads & links

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Assembly

Deposited unit
A: Heme Oxygenase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2513
Polymers30,6121
Non-polymers6382
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.400, 65.400, 121.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assmbly is a monomer.

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Components

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


Mass: 30612.496 Da / Num. of mol.: 1 / Fragment: C-terminal truncated protein
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.91 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, potassium phosphate, potassium cyanide, 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: Apr 23, 2002
RadiationMonochromator: Si (111) double monochrmator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→60.9 Å / Num. all: 12241 / Num. obs: 12207 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1726 / Rsym value: 0.343 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 88285 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.343

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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 1IX3

1ix3


Resolution: 2.4→60.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 1238 random
Rwork0.194 --
all0.199 12271 -
obs0.199 11903 -
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→60.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 38 74 1840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.144
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d19.119
X-RAY DIFFRACTIONc_improper_angle_d0.805
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.229 108 -
Rwork0.236 --
obs-1107 84.8 %
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.119
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.805

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