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- PDB-2q32: Crystal structure of human heme oxygenase-2 C127A (HO-2) -

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Basic information

Entry
Database: PDB / ID: 2q32
TitleCrystal structure of human heme oxygenase-2 C127A (HO-2)
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / HO-2 / HEME Oxygenase / Structural Genomics Medical Relevance / Structural Genomics Community Request / Protein Structure Initiative / PSI / 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 / Resolution: 2.4 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Bitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Comparison of Apo- and Heme-bound Crystal Structures of a Truncated Human Heme Oxygenase-2.
Authors: Bianchetti, C.M. / Yi, L. / Ragsdale, S.W. / Phillips Jr., G.N.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2764
Polymers60,9832
Non-polymers1,2942
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.769, 86.017, 97.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETAA30 - 24030 - 240
2ALAALABB31 - 24031 - 240
DetailsThe biological unit is a dimer (chains A & B in ASU).

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Components

#1: Protein Heme oxygenase 2 / HO-2


Mass: 30491.271 Da / Num. of mol.: 2 / Mutation: C127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hs.284279, HMOX2, HO2 / Plasmid: pGEX 4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P30519, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100


Mass: 646.849 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein solution (5 mg/ml Protein, 0.050 M Potassium chloride, 0.005 M Tris-HCl pH 8.5) mixed in a 1.5:1 ratio with the well solution (40% PEG 1500, 0.20 M Potassium glutamate, 0.10 M ...Details: Protein solution (5 mg/ml Protein, 0.050 M Potassium chloride, 0.005 M Tris-HCl pH 8.5) mixed in a 1.5:1 ratio with the well solution (40% PEG 1500, 0.20 M Potassium glutamate, 0.10 M Triethanolamine, pH 8.5). Cryoprotected with well solution, VAPOR DIFUSSION, HANGING DROP, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→49.148 Å / Num. obs: 28128 / % possible obs: 95.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.082 / Χ2: 1.17 / Net I/σ(I): 13.505
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.383.90.6081.92922450.98378.2
2.38-2.485.40.57124881.01586.5
2.48-2.596.80.48327281.09494.5
2.59-2.737.70.37128781.08299.2
2.73-2.980.26629111.308100
2.9-3.128.10.18129021.424100
3.12-3.448.10.12129311.325100
3.44-3.9380.09829451.131100
3.93-4.957.90.06929741.101100
4.95-49.1487.60.03631261.01599.8

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Phasing

Phasing MRRfactor: 0.478 / Cor.coef. Fo:Fc: 0.475
Highest resolutionLowest resolution
Rotation4 Å49.15 Å
Translation4 Å49.15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N45

1n45


Resolution: 2.4→49.148 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.213 / SU B: 17.022 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1275 5.056 %RANDOM
Rwork0.201 ---
obs0.204 25217 98.431 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.622 Å2
Baniso -1Baniso -2Baniso -3
1--2.315 Å20 Å20 Å2
2---1.049 Å20 Å2
3---3.364 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 70 154 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223770
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9825072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6725.072207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94615689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5851521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022899
X-RAY DIFFRACTIONr_nbd_refined0.1980.21825
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.24
X-RAY DIFFRACTIONr_mcbond_it0.5141.52272
X-RAY DIFFRACTIONr_mcangle_it0.79923520
X-RAY DIFFRACTIONr_scbond_it1.23231688
X-RAY DIFFRACTIONr_scangle_it1.9664.51552
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1675 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.470.5
MEDIUM THERMAL0.632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4620.336820.2631552186487.661
2.462-2.530.363760.2641608179693.764
2.53-2.6030.406840.2511668179497.659
2.603-2.6830.281830.2521600169699.233
2.683-2.770.278800.25915891669100
2.77-2.8670.298780.2415331611100
2.867-2.9750.271890.23214621551100
2.975-3.0960.343760.22314241500100
3.096-3.2330.263870.213621449100
3.233-3.390.29700.20213061376100
3.39-3.5730.288710.19212581329100
3.573-3.7880.276660.18311951261100
3.788-4.0480.266660.17811081174100
4.048-4.370.153610.15810551116100
4.37-4.7840.214530.1719701023100
4.784-5.3420.195490.199879928100
5.342-6.1570.216430.229790833100
6.157-7.5120.21270.208694721100
7.512-10.5060.248200.159552572100
10.506-49.1480.301140.22333735698.596
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38670.9854-0.14862.1547-0.36592.18970.0001-0.0481-0.15870.1784-0.02790.0297-0.0414-0.07590.0278-0.27010.0546-0.0441-0.2374-0.0422-0.177325.65821.81736.717
23.12480.77630.38174.5599-1.65894.44450.02180.00290.20040.1975-0.2365-0.7597-0.21250.88850.2147-0.14370.0096-0.0572-0.06560.0832-0.059849.690215.595629.4417
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA29 - 4229 - 42
21AA43 - 6243 - 62
31AA63 - 13363 - 133
41AA134 - 162134 - 162
51AA163 - 181163 - 181
61AA182 - 203182 - 203
71AA204 - 229204 - 229
81AA230 - 241230 - 241
92BB31 - 4331 - 43
102BB44 - 6544 - 65
112BB66 - 11566 - 115
122BB116 - 132116 - 132
132BB133 - 154133 - 154
142BB155 - 176155 - 176
152BB177 - 196177 - 196
162BB197 - 218197 - 218
172BB219 - 242219 - 242

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