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- PDB-1n3u: Crystal structure of human heme oxygenase 1 (HO-1) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1n3u
TitleCrystal structure of human heme oxygenase 1 (HO-1) in complex with its substrate heme, crystal form B
Componentsheme oxygenase 1
KeywordsOXIDOREDUCTASE / alpha helices / heme-binding site
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / heme oxidation / low-density lipoprotein particle clearance / negative regulation of leukocyte migration / smooth muscle hyperplasia / 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 / negative regulation of leukocyte migration / smooth muscle hyperplasia / 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 / positive regulation of cell migration involved in sprouting angiogenesis / Heme degradation / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of ferroptosis / negative regulation of macroautophagy / cellular response to cadmium ion / The NLRP3 inflammasome / positive regulation of macroautophagy / 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 / positive regulation of smooth muscle cell proliferation / response to nicotine / macroautophagy / negative regulation of smooth muscle cell proliferation / response to hydrogen peroxide / Heme signaling / Iron uptake and transport / Cytoprotection by HMOX1 / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / response to oxidative stress / angiogenesis / Interleukin-4 and Interleukin-13 signaling / intracellular iron ion homeostasis / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLad, L. / Schuller, D.J. / Friedman, J.P. / Li, H. / Ortiz de Montellano, P.R. / Poulos, T.L.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Comparison of the heme-free and -bound crystal structures of human heme oxygenase-1
Authors: Lad, L. / Schuller, D.J. / Shimizu, H. / Friedman, J. / Li, H. / Ortiz de Montellano, P.R. / Poulos, T.L.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal Structure of Human Heme Oxygenase-1
Authors: Schuller, D.J. / Wilks, A. / Ortiz de Montellano, P.R. / Poulos, T.L.
History
DepositionOct 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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)55,1377
Polymers53,7972
Non-polymers1,3395
Water1,56787
1
A: heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5513
Polymers26,8991
Non-polymers6522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5864
Polymers26,8991
Non-polymers6873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.395, 55.920, 79.379
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe enzyme is a monomer

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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, HO1 / Plasmid: delta233-hHO-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: 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: 2.31 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, HEPES, 1,6-hexanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 301K
Crystal grow
*PLUS
Temperature: 28 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.08 Mammonium sulfate1reservoir
2100 mMHEPES1reservoirpH7.5
30.9 %1,6-hexanediol1reservoir
435 mg/mlprotein1drop
520 mMpotassium phosphate1droppH7.4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 1998 / Details: mirrors
RadiationMonochromator: mirrors + nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→78 Å / Num. all: 14937 / Num. obs: 14295 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 64.6 Å2 / Rsym value: 0.074 / Net I/σ(I): 10.1
Reflection shellResolution: 2.58→2.64 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3 / Num. unique all: 674 / Rsym value: 0.566 / % possible all: 94.4
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 78 Å / Num. obs: 14273 / Num. measured all: 100842 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 94.4 % / Rmerge(I) obs: 0.566

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QQ8

1qq8
PDB Unreleased entry


Resolution: 2.58→70 Å / Isotropic thermal model: isotropic / Cross valid method: througout / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 780 -random
Rwork0.225 ---
all0.227 14936 --
obs0.227 14295 96.9 %-
Refinement stepCycle: LAST / Resolution: 2.58→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 89 87 3666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
Refinement
*PLUS
Highest resolution: 2.6 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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