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- PDB-5uc8: Crystal structure of human Heme Oxygenase-2 -

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Basic information

Entry
Database: PDB / ID: 5uc8
TitleCrystal structure of human Heme Oxygenase-2
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / heme oxygenase
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / Heme degradation / RHOA GTPase cycle / specific granule membrane / Iron uptake and transport / Cytoprotection by HMOX1 / response to oxidative stress ...heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / Heme degradation / RHOA GTPase cycle / specific granule membrane / Iron uptake and transport / Cytoprotection by HMOX1 / response to oxidative stress / response to hypoxia / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / metal ion binding / membrane / plasma membrane
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: Cell Host Microbe / Year: 2017
Title: Heme Oxygenase 2 Binds Myristate to Regulate Retrovirus Assembly and TLR4 Signaling.
Authors: Zhu, Y. / Luo, S. / Sabo, Y. / Wang, C. / Tong, L. / Goff, S.P.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme oxygenase 2
B: Heme oxygenase 2
C: Heme oxygenase 2
D: Heme oxygenase 2


Theoretical massNumber of molelcules
Total (without water)105,1474
Polymers105,1474
Non-polymers00
Water12,358686
1
A: Heme oxygenase 2


Theoretical massNumber of molelcules
Total (without water)26,2871
Polymers26,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 2


Theoretical massNumber of molelcules
Total (without water)26,2871
Polymers26,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase 2


Theoretical massNumber of molelcules
Total (without water)26,2871
Polymers26,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heme oxygenase 2


Theoretical massNumber of molelcules
Total (without water)26,2871
Polymers26,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.760, 84.619, 139.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Heme oxygenase 2 / HO-2


Mass: 26286.639 Da / Num. of mol.: 4 / Fragment: residues 1-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX2, HO2 / Production host: Escherichia coli (E. coli)
References: UniProt: P30519, heme oxygenase (biliverdin-producing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris (pH 6.5) and 24% (w/v) PEG 2,000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2016 / Details: LR-Design detector positioner
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 65740 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.24 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Χ2: 1.042 / Net I/σ(I): 16.6 / Num. measured all: 237797
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.073.60.4920.7851100
2.07-2.153.70.3370.8791100
2.15-2.253.70.2430.9271100
2.25-2.373.70.180.963199.9
2.37-2.523.70.1240.981100
2.52-2.713.70.0930.988199.9
2.71-2.993.70.0730.9931100
2.99-3.423.60.0670.9941100
3.42-4.33.50.0730.9911100
4.3-253.40.0370.997198.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q32

2q32


Resolution: 2→24.783 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.12
RfactorNum. reflection% reflection
Rfree0.2509 1748 2.8 %
Rwork0.196 --
obs0.1976 62506 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.28 Å2 / Biso mean: 37.9007 Å2 / Biso min: 17.97 Å2
Refinement stepCycle: final / Resolution: 2→24.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6915 0 0 686 7601
Biso mean---40.82 -
Num. residues----839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077059
X-RAY DIFFRACTIONf_angle_d0.7429489
X-RAY DIFFRACTIONf_chiral_restr0.042983
X-RAY DIFFRACTIONf_plane_restr0.0051251
X-RAY DIFFRACTIONf_dihedral_angle_d17.6814297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05880.28381180.26850335151100
2.0588-2.12520.30271600.2449985158100
2.1252-2.20120.32351470.233149995146100
2.2012-2.28920.27961510.227150275178100
2.2892-2.39330.31111360.219950185154100
2.3933-2.51940.29961470.212550215168100
2.5194-2.67710.28271470.217150615208100
2.6771-2.88350.27791490.215450475196100
2.8835-3.17310.2831400.215550695209100
3.1731-3.63110.2461540.192451045258100
3.6311-4.57010.19671490.161551645313100
4.5701-24.78530.21151500.16755217536798

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