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- PDB-5uc9: Crystal structure of human Heme Oxygenase-2 in complex with Myristate -

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Basic information

Entry
Database: PDB / ID: 5uc9
TitleCrystal structure of human Heme Oxygenase-2 in complex with Myristate
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / heme oxygenase / myristic 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 / membrane / metal ion binding / 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
MYRISTIC ACID / Heme oxygenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 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

Downloads & links

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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)106,0608
Polymers105,1474
Non-polymers9134
Water10,521584
1
A: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5152
Polymers26,2871
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5152
Polymers26,2871
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5152
Polymers26,2871
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5152
Polymers26,2871
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.751, 82.900, 137.051
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: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
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: Apr 10, 2015 / 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: 1.9→25 Å / Num. obs: 68092 / % possible obs: 97.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.83 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Χ2: 1.039 / Net I/σ(I): 14.1 / Num. measured all: 246452
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.973.60.5340.773191.6
1.97-2.053.60.3470.886193.3
2.05-2.143.60.2510.931195.7
2.14-2.253.60.1870.958197.7
2.25-2.393.60.1370.974199.3
2.39-2.583.70.1010.987199.5
2.58-2.843.70.0760.993199.7
2.84-3.253.60.0560.995199.8
3.25-4.093.60.050.995199.6
4.09-253.50.0240.999197

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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: 1.903→25 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2437 4978 7.32 %
Rwork0.1884 --
obs0.1924 68033 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.45 Å2 / Biso mean: 33.3945 Å2 / Biso min: 15.63 Å2
Refinement stepCycle: final / Resolution: 1.903→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6923 0 64 584 7571
Biso mean--37.51 37.45 -
Num. residues----840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087127
X-RAY DIFFRACTIONf_angle_d0.8569559
X-RAY DIFFRACTIONf_chiral_restr0.049984
X-RAY DIFFRACTIONf_plane_restr0.0051256
X-RAY DIFFRACTIONf_dihedral_angle_d17.0164351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9034-1.92510.31351420.26561768191083
1.9251-1.94770.32591470.24791948209591
1.9477-1.97150.36671450.24151999214493
1.9715-1.99640.28911640.22161980214493
1.9964-2.02270.27751610.21432013217494
2.0227-2.05030.24681420.20822013215594
2.0503-2.07960.2541730.21471999217295
2.0796-2.11070.28881610.2112045220696
2.1107-2.14360.27191690.21032073224297
2.1436-2.17870.27341670.19892055222297
2.1787-2.21630.261460.21312138228498
2.2163-2.25660.31541850.2132085227098
2.2566-2.29990.23391630.20022117228099
2.2999-2.34680.23861730.200321492322100
2.3468-2.39780.26581670.196821272294100
2.3978-2.45360.25131650.1992142230799
2.4536-2.51490.25361840.199721572341100
2.5149-2.58280.26781610.196721632324100
2.5828-2.65870.26791690.205721432312100
2.6587-2.74440.25981610.198521372298100
2.7444-2.84240.27931750.201221622337100
2.8424-2.9560.25271750.206921472322100
2.956-3.09030.25951660.205821902356100
3.0903-3.25290.27611790.205621512330100
3.2529-3.45630.24281750.195721802355100
3.4563-3.72230.2231710.179321822353100
3.7223-4.09540.24791700.16782192236299
4.0954-4.68470.17741690.14712183235299
4.6847-5.88950.23791730.17262197237098
5.8895-25.00770.18291800.15352220240095

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