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- PDB-1s13: Human Heme Oxygenase Oxidatition of alpha- and gamma-meso-Phenylhemes -

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Basic information

Entry
Database: PDB / ID: 1s13
TitleHuman Heme Oxygenase Oxidatition of alpha- and gamma-meso-Phenylhemes
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / heme oxygenase-1 / heme degradation
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / heme oxidation / low-density lipoprotein particle clearance / smooth muscle hyperplasia / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / cellular response to cisplatin / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / heme oxidation / low-density lipoprotein particle clearance / smooth muscle hyperplasia / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / 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 / heme catabolic process / positive regulation of epithelial cell apoptotic process / endothelial cell proliferation / epithelial cell apoptotic process / negative regulation of ferroptosis / erythrocyte homeostasis / Heme degradation / positive regulation of cell migration involved in sprouting angiogenesis / NFE2L2 regulating anti-oxidant/detoxification enzymes / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of macroautophagy / cellular response to cadmium ion / positive regulation of macroautophagy / The NLRP3 inflammasome / regulation of angiogenesis / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of chemokine production / negative regulation of cytokine production involved in inflammatory response / response to nicotine / positive regulation of smooth muscle cell proliferation / macroautophagy / negative regulation of smooth muscle cell proliferation / Heme signaling / Iron uptake and transport / Cytoprotection by HMOX1 / response to hydrogen peroxide / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / Interleukin-4 and Interleukin-13 signaling / angiogenesis / response to oxidative stress / mitochondrial outer membrane / intracellular iron ion homeostasis / positive regulation of canonical NF-kappaB signal transduction / 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 / metal ion binding / identical protein binding / nucleus / membrane / 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
2-PHENYLHEME / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsWang, J. / Niemevz, F. / Lad, L. / Buldain, G. / Poulos, T.L. / Ortiz de Montellano, P.R.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Human heme oxygenase oxidation of 5- and 15-phenylhemes.
Authors: Wang, J. / Niemevz, F. / Lad, L. / Huang, L. / Alvarez, D.E. / Buldain, G. / Poulos, T.L. / Ortiz de Montellano, P.R.
History
DepositionJan 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Remark 600heterogen The outer propionate is disordered in the ligand 2FH

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme oxygenase 1
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1824
Polymers53,7972
Non-polymers1,3852
Water2,900161
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5912
Polymers26,8991
Non-polymers6931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5912
Polymers26,8991
Non-polymers6931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.070, 75.750, 107.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme oxygenase 1 / HO-1


Mass: 26898.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1 or HO1 or HO / Plasmid: pCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-2FH / 2-PHENYLHEME


Mass: 692.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H36FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulphate, HEPES, hexanediol, jeffamine ED600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 119 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 18, 2003 / Details: yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 20845 / Num. obs: 20818 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.066 / Rsym value: 0.055 / Net I/σ(I): 21.1
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2477 / Rsym value: 0.046 / % possible all: 95

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qq8

1qq8
PDB Unreleased entry


Resolution: 2.29→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1006 -random
Rwork0.21 ---
all-20845 --
obs-20818 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 86 161 3737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.1
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.29-2.370.3471040.3071X-RAY DIFFRACTION19299.27
2.37-2.470.347830.2923X-RAY DIFFRACTION19629.42
2.47-2.580.35851200.2767X-RAY DIFFRACTION19299.27
2.58-2.720.30281090.263X-RAY DIFFRACTION19419.32
2.72-2.890.3067810.2591X-RAY DIFFRACTION19929.57
2.89-3.110.3031080.2482X-RAY DIFFRACTION19619.41
3.11-3.420.2769930.2393X-RAY DIFFRACTION19839.52
3.42-3.920.2403960.2121X-RAY DIFFRACTION19979.59
3.92-4.930.20221080.1871X-RAY DIFFRACTION20139.66
4.93-500.2461040.2161X-RAY DIFFRACTION210510.11

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