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- PDB-1ni6: Comparisions of the Heme-Free and-Bound Crystal Structures of Hum... -

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Basic information

Entry
Database: PDB / ID: 1ni6
TitleComparisions of the Heme-Free and-Bound Crystal Structures of Human Heme Oxygenase-1
ComponentsHeme oxygenase 1
KeywordsOXYGEN STORAGE/TRANSPORT / heme oxygenase-1 / heme degradation / OXYGEN STORAGE-TRANSPORT COMPLEX
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 / positive regulation of cell migration involved in sprouting angiogenesis / epithelial cell apoptotic process / 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 / Iron uptake and transport / Heme signaling / 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
trehalose / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLad, L. / Schuller, D.J. / Friedman, J. / Li, H. / Shimizu, H. / Ortiz de Montellano, P.R. / Poulos, T.L.
CitationJournal: 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.
History
DepositionDec 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)104,0806
Polymers103,7024
Non-polymers3782
Water8,107450
1
A: Heme oxygenase 1


Theoretical massNumber of molelcules
Total (without water)25,9261
Polymers25,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase 1


Theoretical massNumber of molelcules
Total (without water)25,9261
Polymers25,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3033
Polymers25,9261
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heme oxygenase 1


Theoretical massNumber of molelcules
Total (without water)25,9261
Polymers25,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.211, 55.507, 108.001
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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


Mass: 25925.568 Da / Num. of mol.: 4 / Fragment: apo form
Source method: isolated from a genetically manipulated source
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: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulphate, 1,6 hexane diol, HEPES, water, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 301K

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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: Aug 17, 2001 / 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: 2.1→50 Å / Num. all: 52492 / Num. obs: 49421 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.049 / Net I/σ(I): 20.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.67 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.02 / Num. unique all: 2309 / Rsym value: 0.49 / % possible all: 87.4

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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: 1QQ8

1qq8
PDB Unreleased entry


Resolution: 2.1→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 3159 6.4 %random
Rwork0.2168 ---
obs-49333 93.9 %-
Displacement parametersBiso mean: 46.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7055 0 24 450 7529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006106
X-RAY DIFFRACTIONc_angle_d1.13241
X-RAY DIFFRACTIONc_mcbond_it1.0421.5
X-RAY DIFFRACTIONc_mcangle_it1.6832
X-RAY DIFFRACTIONc_scbond_it1.6452
X-RAY DIFFRACTIONc_scangle_it2.4382.5
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 (%)
2.1-2.180.33612480.297944049.4
2.18-2.260.31552360.263744429.47
2.26-2.370.29612330.242144589.51
2.37-2.490.32362250.2544299.51
2.49-2.650.29912350.233645269.66
2.65-2.850.25922270.210546599.94
2.85-3.140.28352550.2294484010.33
3.14-3.590.26842660.2186496210.59
3.59-4.520.22852730.1836502310.72
4.52-500.25082720.2066512010.92

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