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- PDB-5uca: Crystal structure of human Heme Oxygenase-2 in complex with Laurate -

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Basic information

Entry
Database: PDB / ID: 5uca
TitleCrystal structure of human Heme Oxygenase-2 in complex with Laurate
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / heme oxygenase / lauric acid
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
LAURIC ACID / Heme oxygenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.117 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7487
Polymers105,1474
Non-polymers6013
Water7,458414
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,2871
Non-polymers2001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,2871
Non-polymers2001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,2871
Non-polymers2001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.363, 83.920, 138.297
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 30-242
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: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H24O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris (pH 6.5) and 24% (w/v) PEG 2000 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: 2.1→25 Å / Num. obs: 51449 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.23 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.037 / Rrim(I) all: 0.075 / Χ2: 1.024 / Net I/σ(I): 17 / Num. measured all: 197403
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.183.50.3850.869199.2
2.18-2.263.60.2840.918199.7
2.26-2.363.70.2040.963199.9
2.36-2.493.80.1480.979199.9
2.49-2.653.90.1150.987199.9
2.65-2.8540.0880.9921100
2.85-3.1440.0710.9941100
3.14-3.5940.0690.9921100
3.59-4.523.80.0580.994199.6
4.52-253.80.0250.999196.1

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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: 5UC8

5uc8


Resolution: 2.117→24.65 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58
RfactorNum. reflection% reflection
Rfree0.2492 1445 2.81 %
Rwork0.1933 --
obs0.1949 51395 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.07 Å2 / Biso mean: 40.7213 Å2 / Biso min: 16.3 Å2
Refinement stepCycle: final / Resolution: 2.117→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6915 0 42 414 7371
Biso mean--46.14 41.61 -
Num. residues----839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077098
X-RAY DIFFRACTIONf_angle_d0.7979528
X-RAY DIFFRACTIONf_chiral_restr0.043983
X-RAY DIFFRACTIONf_plane_restr0.0051254
X-RAY DIFFRACTIONf_dihedral_angle_d19.4044327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1169-2.19260.33311370.25314626476393
2.1926-2.28030.29621470.238549975144100
2.2803-2.3840.30921320.211749675099100
2.384-2.50960.31311490.214450085157100
2.5096-2.66660.28981430.218150105153100
2.6666-2.87220.27931470.218350225169100
2.8722-3.16070.271440.216950295173100
3.1607-3.61690.25821500.196950625212100
3.6169-4.55220.19791470.16351145261100
4.5522-24.65180.20661490.16345115526496

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