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- PDB-1oyk: Crystal Structures of the Ferric, Ferrous, and Ferrous-NO Forms o... -

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Entry
Database: PDB / ID: 1oyk
TitleCrystal Structures of the Ferric, Ferrous, and Ferrous-NO Forms of the Asp140Ala Mutant of Human Heme Oxygenase-1: Catalytic Implications
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / heme oxygenase / 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 / 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: 2.59 Å
AuthorsLad, L. / Wang, J. / Li, H. / Friedman, J. / Ortiz de Montellano, P.R. / Poulos, T.L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structures of the ferric, ferrous, and ferrous-NO forms of the Asp140Ala mutant of human heme oxygenase-1: catalytic implications
Authors: Lad, L. / Wang, J. / Li, H. / Friedman, J. / Bhaskar, B. / Ortiz de Montellano, P.R. / Poulos, T.L.
History
DepositionApr 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,9424
Polymers53,7092
Non-polymers1,2332
Water1,78399
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4712
Polymers26,8551
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4712
Polymers26,8551
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.665, 77.662, 100.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Heme oxygenase 1 / E.C.1.14.99.3 / HO-1 / heme oxygenase (decyclizing) 1


Mass: 26854.605 Da / Num. of mol.: 2 / Fragment: residues 1-233 of SWS P09601 / Mutation: Asp140ala
Source method: isolated from a genetically manipulated source
Details: Heme-complexed / Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1 / Plasmid: pCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammomium sulphate, 1,6 hexane-diol, HEPES, water, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 301K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.08 Mammonium sulfate1reservoir
2100 mMHEPES1reservoirpH7.5
30.9 %(v/v)1,6-hexanediol1reservoir
445 mg/mlprotein1drop
520 mMpotassium phosphate1droppH7.4

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Data collection

DiffractionMean temperature: 119 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 2002 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 33028 / Num. obs: 14071 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.066 / Net I/σ(I): 19.8
Reflection
*PLUS
Num. obs: 33028 / Num. measured all: 135214 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.01

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQ8

1qq8
PDB Unreleased entry


Resolution: 2.59→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3087 --random
Rwork0.2335 ---
all0.23351 14071 --
obs0.23351 14071 97.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 86 99 3669
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg_1.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2.59-2.680.4565530.335113099.3
2.68-2.790.3712660.30113269.42
2.79-2.920.3977740.271412929.18
2.92-3.070.3086730.272713159.35
3.07-3.260.3695720.267113139.33
3.26-3.510.313700.255613259.42
3.51-3.870.4268530.28410827.69
3.87-4.430.2926680.187713389.51
4.43-5.580.2589810.205513719.74
5.58-500.2491850.1994141310.04
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS

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