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- PDB-4wmh: Structure of heme oxygenase-2 containing residues 1-288 lacking t... -

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Basic information

Entry
Database: PDB / ID: 4wmh
TitleStructure of heme oxygenase-2 containing residues 1-288 lacking the membrane spanning region
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / HO2 / Heme oxygenase / Oxygenase / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsBianchetti, C.M. / Li, Y. / Ragsdale, S.W. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL102662-01 United States
CitationJournal: To Be Published
Title: Structure of heme oxygenase-2 containing residues 1-288 lacking the membrane spanning region
Authors: Bianchetti, C.M. / Li, Y. / Ragsdale, S.W. / Phillips Jr., G.N.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations / Other
Revision 2.0Sep 27, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site_anisotrop / entity_src_gen ...atom_site_anisotrop / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3102
Polymers24,2751
Non-polymers351
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.690, 35.690, 366.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Heme oxygenase 2 / HO-2


Mass: 24274.520 Da / Num. of mol.: 1 / Fragment: UNP residues 31-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX2, HO2 / Plasmid: PGEX 4T-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30519, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 1.5K and 100mM BTP pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→91.68 Å / Num. obs: 8270 / % possible obs: 99.82 % / Redundancy: 25.3 % / Net I/σ(I): 17.36

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QPP

2qpp


Resolution: 2.5→91.68 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 33.904 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.655 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 936 10.2 %RANDOM
Rwork0.2261 8270 --
obs0.2308 8270 99.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 52.899 Å2 / Biso min: 38.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å2-0 Å2-0 Å2
2--1.74 Å2-0 Å2
3----3.48 Å2
Refinement stepCycle: final / Resolution: 2.5→91.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 1 6 1715
Biso mean--91.52 58.74 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191753
X-RAY DIFFRACTIONr_bond_other_d0.0010.021664
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9572357
X-RAY DIFFRACTIONr_angle_other_deg0.7333832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9755208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28424.84597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3315328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.341510
X-RAY DIFFRACTIONr_chiral_restr0.0530.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_mcbond_it1.4755.185829
X-RAY DIFFRACTIONr_mcbond_other1.4755.183828
X-RAY DIFFRACTIONr_mcangle_it2.3997.7751035
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 71 -
Rwork0.344 604 -
all-675 -
obs--99.7 %
Refinement TLS params.Method: refined / Origin x: -2.191 Å / Origin y: -16.322 Å / Origin z: -26.112 Å
111213212223313233
T0.0484 Å20.0287 Å2-0.0225 Å2-0.3049 Å2-0.0988 Å2--0.0568 Å2
L1.2646 °20.0225 °2-0.8212 °2-1.4697 °2-1.814 °2--8.4142 °2
S0.0819 Å °-0.1329 Å °-0.0229 Å °0.0037 Å °0.0191 Å °0.1599 Å °0.1941 Å °-0.246 Å °-0.101 Å °

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