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- PDB-3i9u: Crystal structure of the rat heme oxygenase (HO-1) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3i9u
TitleCrystal structure of the rat heme oxygenase (HO-1) in complex with heme binding dithioerythritol (DTE)
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / heme oxygenase / inhibitor / isozyme / Endoplasmic reticulum / Heme / Iron / Metal-binding / Microsome / Phosphoprotein
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / arachidonate omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / cellular response to cisplatin ...Regulation of HMOX1 expression and activity / arachidonate omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / cellular response to cisplatin / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / phospholipase D activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / negative regulation of ferroptosis / epithelial cell apoptotic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / response to nicotine / liver regeneration / macroautophagy / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to hydrogen peroxide / caveola / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / cellular response to heat / angiogenesis / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / response to oxidative stress / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / 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
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMatsui, T. / Unno, M. / Ikeda-Saito, M.
CitationJournal: Inorg.Chem. / Year: 2010
Title: Dioxygen activation for the self-degradation of heme: reaction mechanism and regulation of heme oxygenase.
Authors: Matsui, T. / Iwasaki, M. / Sugiyama, R. / Unno, M. / Ikeda-Saito, M.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)31,0663
Polymers30,2951
Non-polymers7712
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.882, 65.882, 120.244
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 / HO-1 / HSP32


Mass: 30295.268 Da / Num. of mol.: 1 / Fragment: UNP residues 1-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: pMW / Production host: Escherichia coli (E. coli)
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-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 3.2M sodium formate, 10mM sodium azide, 5mM DTV, pH7.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 14964 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 30.585 Å2 / Rsym value: 0.062 / Net I/σ(I): 32.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 7.04 / Num. unique all: 1454 / Rsym value: 0.329 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I9T

3i9t


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.826 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22266 754 5.1 %RANDOM
Rwork0.16683 ---
obs0.16961 14140 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.132 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20.88 Å20 Å2
2--1.76 Å20 Å2
3----2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 51 101 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221812
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9132.0342468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71923.79387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25515297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.261511
X-RAY DIFFRACTIONr_chiral_restr0.1290.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211394
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.51060
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91221701
X-RAY DIFFRACTIONr_scbond_it3.173752
X-RAY DIFFRACTIONr_scangle_it5.0264.5767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 49 -
Rwork0.207 1017 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1533-0.1731-0.19060.39670.35351.2768-0.0089-0.0190.01730.00230.0026-0.00790.0551-0.00360.00630.00390.004600.03680.00460.0073-7.2903-36.0557-164.0508
23.04710.0059-0.06673.74421.52192.6891-0.13360.23670.01090.04460.0446-0.3173-0.1965-0.13050.08890.02970.0021-0.02830.0517-0.01020.0526-2.202-27.3906-168.0463
32.6724.702-7.40488.2743-13.030520.521-0.08610.27480.1445-0.15580.48590.25640.2428-0.7579-0.39980.0215-0.037-0.02090.07530.01860.1052-3.2904-33.0346-168.9029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 222
2X-RAY DIFFRACTION2A300
3X-RAY DIFFRACTION3A2001

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