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- PDB-1s8c: Crystal structure of human heme oxygenase in a complex with biliv... -

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Basic information

Entry
Database: PDB / ID: 1s8c
TitleCrystal structure of human heme oxygenase in a complex with biliverdine
ComponentsHeme oxygenase 1HMOX1
KeywordsOXIDOREDUCTASE / heme oxygenase-1 / heme degradation
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / 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 / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / 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 / endothelial cell proliferation / erythrocyte homeostasis / positive regulation of epithelial cell apoptotic process / Heme degradation / epithelial cell apoptotic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of macroautophagy / positive regulation of cell migration involved in sprouting angiogenesis / 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 / cellular response to cadmium ion / response to nicotine / negative regulation of smooth muscle cell proliferation / macroautophagy / Iron uptake and transport / 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 / cellular response to hypoxia / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / Interleukin-4 and Interleukin-13 signaling / response to oxidative stress / intracellular iron ion homeostasis / mitochondrial outer membrane / 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 / membrane / identical protein binding / metal ion 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
BILIVERDINE IX ALPHA / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLad, L. / Friedman, J. / Li, H. / Bhaskar, B. / Ortiz de Montellano, P.R. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of Human Heme Oxygenase-1 in a Complex with Biliverdin
Authors: Lad, L. / Friedman, J. / Li, H. / Bhaskar, B. / Ortiz De Montellano, P.R. / Poulos, T.L.
History
DepositionFeb 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,1775
Polymers107,5944
Non-polymers5831
Water5,855325
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4812
Polymers26,8991
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 1


Theoretical massNumber of molelcules
Total (without water)26,8991
Polymers26,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase 1


Theoretical massNumber of molelcules
Total (without water)26,8991
Polymers26,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heme oxygenase 1


Theoretical massNumber of molelcules
Total (without water)26,8991
Polymers26,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.413, 56.461, 109.751
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Heme oxygenase 1 / HMOX1 / HO-1


Mass: 26898.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO1, HO / Plasmid: pCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, hepes, 1,6 hexanediol, water, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 119 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 64336 / Num. obs: 55646 / % possible obs: 86.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.062 / Rsym value: 0.056 / Net I/σ(I): 17.3
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5768 / Rsym value: 0.056 / % possible all: 90.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1qq8

1qq8
PDB Unreleased entry


Resolution: 2.19→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2814 -random
Rwork0.24 ---
all-64336 --
obs-55646 86.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.285 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.248 Å
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6973 0 43 325 7341

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