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- PDB-1ulx: Partially photolyzed structure of CO-bound heme-heme oxygenase complex -

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Basic information

Entry
Database: PDB / ID: 1ulx
TitlePartially photolyzed structure of CO-bound heme-heme oxygenase complex
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / photolyzed intermediate / cryotrapped
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: CO-trapping site in heme oxygenase revealed by photolysis of its co-bound heme complex: mechanism of escaping from product inhibition
Authors: Sugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
History
DepositionSep 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.4Oct 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)31,3135
Polymers30,6121
Non-polymers7014
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.900, 65.900, 120.100
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: 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: 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.88 Å3/Da / Density % sol: 57.01 %
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

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Data collection

DiffractionMean temperature: 35 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 19139 / Num. obs: 17805 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.06 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.07 Å / Num. unique all: 1779 / Rsym value: 0.359 / % possible all: 87

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1IX4

1ix4


Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The positions of photolyzed carbon monoxide are not refined.
RfactorNum. reflectionSelection details
Rfree0.239 863 random
Rwork0.207 --
all0.209 19139 -
obs0.209 17805 -
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 49 105 1865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0068
X-RAY DIFFRACTIONc_bond_d1.2036
X-RAY DIFFRACTIONc_dihedral_angle_d18.534
X-RAY DIFFRACTIONc_improper_angle_d0.7737
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.3311 94 -
Rwork0.294 --
obs-1744 84.3 %

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