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- PDB-1dve: CRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH HEME -

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Basic information

Entry
Database: PDB / ID: 1dve
TitleCRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH HEME
ComponentsHEME OXYGENASE-1
KeywordsOXIDOREDUCTASE / ALL ALPHA / PROTEIN-SUBSTRATE 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsSugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
Citation
Journal: FEBS Lett. / Year: 2000
Title: Crystal structure of rat heme oxygenase-1 in complex with heme.
Authors: Sugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / Noguchi, M. / Fukuyama, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-ray Diffraction Studies on the Water Soluble Form of Rat Heme Oxygenase-1 in Complex with Heme
Authors: Omata, Y. / Asada, S. / Sakamoto, H. / Fukuyama, K. / Noguchi, M.
History
DepositionJan 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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

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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)31,2292
Polymers30,6121
Non-polymers6161
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.139, 56.139, 183.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HEME OXYGENASE-1 / HO-1


Mass: 30612.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: EXPRESSED AS RESIDUES 1-267 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, TRIS-HCL, SODIUM ACETATE, CRYO:ADD GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7
Details: Omata, Y., (1998) Acta Crystallogr., Sect.D, 54, 1017.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
250 mMpotassium phosphate1drop
30.1 MTris1reservoir
430 %PEG40001reservoir
50.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.89
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 7, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 2.4→27.75 Å / Num. all: 12260 / Num. obs: 12148 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.68 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.05 % / Rmerge(I) obs: 0.174 / Num. unique all: 577 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 69033
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→27.75 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 621 -RANDOM
Rwork0.214 ---
all-12260 --
obs-12104 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.4→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 43 60 1845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.086
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_torsion_deg18.53
X-RAY DIFFRACTIONc_torsion_impr_deg0.759
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.214 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.086

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