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- PDB-1irm: Crystal structure of apo heme oxygenase-1 -

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Basic information

Entry
Database: PDB / ID: 1irm
TitleCrystal structure of apo heme oxygenase-1
Componentsapo heme oxygenase-1
KeywordsOXIDOREDUCTASE / disordered alpha helix / apo form of hemoprotein
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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSugishima, M. / Sakamoto, H. / Kakuta, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystal structure of rat apo-heme oxygenase-1 (HO-1): mechanism of heme binding in HO-1 inferred from structural comparison of the apo and heme complex forms
Authors: Sugishima, M. / Sakamoto, H. / Kakuta, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K.
#1: 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.
#2: 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
DepositionOct 9, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2002Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: apo heme oxygenase-1
A: apo heme oxygenase-1
B: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)91,8373
Polymers91,8373
Non-polymers00
Water1,56787
1
C: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)30,6121
Polymers30,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)30,6121
Polymers30,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: apo heme oxygenase-1


Theoretical massNumber of molelcules
Total (without water)30,6121
Polymers30,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.210, 70.210, 140.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein apo heme oxygenase-1 / HO-1


Mass: 30612.496 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, PEG400, HEPES, stronthium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 Mammonium sulfate1reservoir
22 %PEG4001reservoir
35 mM1reservoirSrCl2
40.1 MHEPES-NaOH1reservoirpH8.0
520 mg/mlprotein1drop
620 mMTris-HCl1droppH7.4
750 mM1dropKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.709 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2000
RadiationMonochromator: Si(111) double monochrometor / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.709 Å / Relative weight: 1
ReflectionResolution: 2.55→46.625 Å / Num. all: 25283 / Num. obs: 25283 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3692 / Rsym value: 0.25 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 93875 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.25

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Processing

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

1dve


Resolution: 2.55→46.625 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: To solve the structure of merohedral twinning crystal, LSQ refinement target used as ( Fo - k( sqrt 0.55Fc^2 + 0.45Fc'^2] ) )^2
RfactorNum. reflection% reflectionSelection details
Rfree0.3068 1110 4.6 %random but, the pairs of twin related reflections are in the same set
Rwork0.2024 ---
all0.204 24264 --
obs0.204 24264 96 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.294 Å2-8.294 Å216.588 Å2
2---7.906 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.55→46.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 0 87 4836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00876
X-RAY DIFFRACTIONc_angle_deg1.464
X-RAY DIFFRACTIONc_dihedral_angle_d22.26
X-RAY DIFFRACTIONc_improper_angle_d0.968
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.55-2.640.3853994.570.3222068499885.6
2.75-3.020.36262050.2815492094.8
3.02-3.460.32172250.2292500399.2
3.46-4.360.28392350.1687505099.9
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.968
LS refinement shell
*PLUS
Rfactor Rfree: 0.3853 / Rfactor Rwork: 0.322

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