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- PDB-3hok: X-ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2... -

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Basic information

Entry
Database: PDB / ID: 3hok
TitleX-ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: A Novel, Inducible Binding Mode
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / protein-inhibitor complex / alpha helices / Endoplasmic reticulum / Heme / Iron / Metal-binding / Microsome / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxygenase (biliverdin-producing) / smooth muscle hyperplasia / heme oxidation / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Regulation of HMOX1 expression and activity / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxygenase (biliverdin-producing) / smooth muscle hyperplasia / heme oxidation / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / heme catabolic process / cellular response to arsenic-containing substance / positive regulation of epithelial cell apoptotic process / endothelial cell proliferation / erythrocyte homeostasis / negative regulation of ferroptosis / epithelial cell apoptotic process / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / positive regulation of cell migration involved in sprouting angiogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of macroautophagy / The NLRP3 inflammasome / positive regulation of macroautophagy / Purinergic signaling in leishmaniasis infection / regulation of angiogenesis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of chemokine production / cellular response to cadmium ion / response to nicotine / Iron uptake and transport / macroautophagy / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / Heme signaling / response to hydrogen peroxide / Cytoprotection by HMOX1 / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / Interleukin-4 and Interleukin-13 signaling / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / mitochondrial outer membrane / response to oxidative stress / intracellular signal transduction / 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 / extracellular space / nucleoplasm / identical protein binding / membrane / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-Q80 / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsRahman, M.N. / Jia, Z.
CitationJournal: J.Med.Chem. / Year: 2009
Title: X-ray crystal structure of human heme oxygenase-1 with (2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: a novel, ...Title: X-ray crystal structure of human heme oxygenase-1 with (2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: a novel, inducible binding mode.
Authors: Rahman, M.N. / Vlahakis, J.Z. / Vukomanovic, D. / Szarek, W.A. / Nakatsu, K. / Jia, Z.
History
DepositionJun 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5145
Polymers53,7972
Non-polymers1,7173
Water3,351186
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5152
Polymers26,8991
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9993
Polymers26,8991
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.072, 54.592, 71.884
Angle α, β, γ (deg.)90.00, 94.641, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme oxygenase 1 / HO-1


Mass: 26898.615 Da / Num. of mol.: 2 / Fragment: Residues 1-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO, HO1 / Plasmid: Delta 233-HHO-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-Q80 / 2-({[(2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methyl}sulfanyl)-5-(trifluoromethyl)pyridine


Mass: 483.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21ClF3N3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: 2.16 M ammonium sulfate, 1.15% 1,6-hexanediol, 0.1 M HEPES, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2008
Details: Bent triangular asymmetric cut Si(111) monochromater provides horizontal focusing. Rh-coated Si mirror for vertical focusing.
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 19633 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 17.31
Reflection shellResolution: 2.19→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.371 / Rsym value: 0.355 / % possible all: 68.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N3U

1n3u


Resolution: 2.19→43.42 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.412 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28894 1018 5.2 %RANDOM
Rwork0.22207 ---
obs0.22567 18614 88.4 %-
all-19633 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.644 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å2-1.38 Å2
2---3.33 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.19→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 118 186 3802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0472.0465053
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11223.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07615637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg191526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212839
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_it0.5041.52147
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93423457
X-RAY DIFFRACTIONr_scbond_it1.12431568
X-RAY DIFFRACTIONr_scangle_it1.8834.51596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 41 -
Rwork0.234 799 -
obs-840 52.4 %

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