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- PDB-1j02: Crystal Structure of Rat Heme Oxygenase-1-Heme Bound to NO -

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Basic information

Entry
Database: PDB / ID: 1j02
TitleCrystal Structure of Rat Heme Oxygenase-1-Heme Bound to NO
ComponentsHEME OXYGENASE 1
KeywordsOXIDOREDUCTASE / alpha helix / O2-analog bound form
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
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSugishima, M. / Fukuyama, K.
CitationJournal: 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.
History
DepositionOct 28, 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)31,2894
Polymers30,6121
Non-polymers6763
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.370, 65.370, 121.010
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


Mass: 30612.496 Da / Num. of mol.: 1 / Fragment: C-terminal truncated fragment
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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.67 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, potassium phosphate, sodium azide, 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: Oct 8, 2002
RadiationMonochromator: Si(111) double monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 33605 / Num. obs: 32251 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 18.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.346 / Num. unique all: 2919 / Rsym value: 0.346 / % possible all: 87.9
Reflection
*PLUS
% possible obs: 99.8 %
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IVJ

1ivj


Resolution: 1.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1599 4.7 %random
Rwork0.201 ---
obs0.202 32211 --
all-33670 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.534 Å2-1.138 Å20 Å2
2---3.713 Å20 Å2
3---7.247 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 47 167 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.1391.5
X-RAY DIFFRACTIONc_mcangle_it1.6922
X-RAY DIFFRACTIONc_scbond_it1.9742
X-RAY DIFFRACTIONc_scangle_it2.9462.5
LS refinement shellResolution: 1.7→1.76 Å
RfactorNum. reflection% reflection
Rfree0.295 158 4.74 %
Rwork0.254 2894 -
obs-2894 86.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2hem.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4nmo.param
Software
*PLUS
Version: 1.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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