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- PDB-2qpp: Crystal structure of human heme oxygenase-2 C127A (HO-2) with bou... -

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Basic information

Entry
Database: PDB / ID: 2qpp
TitleCrystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme
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 / Endoplasmic reticulum / Iron / Metal-binding / Microsome
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
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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
DepositionJul 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2164
Polymers60,9832
Non-polymers1,2332
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1082
Polymers30,4911
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1082
Polymers30,4911
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.977, 85.094, 97.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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: 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 51.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (5 mg/ml Protein, 1:1 ratio HEME, 2% DMSO, 0.050 M Potassium chloride, 0.050 M Tris-HCl pH 7.5) mixed in a 1.5:1 ratio with the Well solution (33% PEG DME 500, 0.020 M ...Details: Protein solution (5 mg/ml Protein, 1:1 ratio HEME, 2% DMSO, 0.050 M Potassium chloride, 0.050 M Tris-HCl pH 7.5) mixed in a 1.5:1 ratio with the Well solution (33% PEG DME 500, 0.020 M Magnesium chloride, 0.10 M HEPES pH 7.5). Cryoprotected with well solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2007 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.32→42.413 Å / Num. obs: 24030 / % possible obs: 85.6 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.083 / Χ2: 1.039 / Net I/σ(I): 16.268
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.32-2.41.80.7150.7767521.13727.4
2.4-2.53.10.81514820.96153.6
2.5-2.615.30.65321270.96677.1
2.61-2.7590.56226620.99695.8
2.75-2.9213.40.41627751.037100
2.92-3.1514.80.26828021.099100
3.15-3.4714.90.15327781.065100
3.47-3.9714.50.08528321.011100
3.97-513.20.07128331.06799.3
5-42.41313.50.04929871.00499.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.97 Å39.02 Å
Translation2.97 Å39.02 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q32

2q32


Resolution: 2.61→40.962 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.213 / SU B: 20.685 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.549 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1005 5.15 %RANDOM
Rwork0.202 ---
obs0.205 19515 99.364 %-
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: 65.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---1.216 Å20 Å2
3---1.555 Å2
Refinement stepCycle: LAST / Resolution: 2.61→40.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 86 83 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223734
X-RAY DIFFRACTIONr_angle_refined_deg0.9512.0295049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.475433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97125200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54215676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2421520
X-RAY DIFFRACTIONr_chiral_restr0.070.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022895
X-RAY DIFFRACTIONr_nbd_refined0.1820.21653
X-RAY DIFFRACTIONr_nbtor_refined0.290.22569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.24
X-RAY DIFFRACTIONr_mcbond_it0.73232238
X-RAY DIFFRACTIONr_mcangle_it1.23443448
X-RAY DIFFRACTIONr_scbond_it0.85941735
X-RAY DIFFRACTIONr_scangle_it1.16741597
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 (%)
2.61-2.6780.413690.3051290144294.244
2.678-2.7510.324650.2851291137498.69
2.751-2.830.294640.2691299136499.927
2.83-2.9170.263770.25312221299100
2.917-3.0120.248690.23712041273100
3.012-3.1170.279670.2291157122599.918
3.117-3.2340.281710.21211241195100
3.234-3.3650.289540.20710891143100
3.365-3.5140.247580.21410661124100
3.514-3.6840.253550.199921047100
3.684-3.8810.254630.1949501013100
3.881-4.1140.286440.184914958100
4.114-4.3950.173520.16984790599.337
4.395-4.7430.208450.18179885598.596
4.743-5.1890.208440.18973578099.872
5.189-5.7890.267350.231690725100
5.789-6.6630.398260.222611637100
6.663-8.1070.258220.189534556100
8.107-11.2470.139120.14442844199.773
11.247-40.9620.418130.21826928499.296
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)
13.79340.81890.19462.6104-0.15342.5292-0.00440.2683-0.2849-0.00170.0709-0.01750.1109-0.1057-0.0664-0.12760.0463-0.0738-0.1631-0.0739-0.064525.365921.78486.633
23.71161.3460.40045.5164-0.96463.0735-0.11870.02610.22580.0858-0.0307-0.5656-0.30910.62850.1495-0.1132-0.0111-0.0587-0.08770.0287-0.137149.526416.165929.0624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 86
2X-RAY DIFFRACTION1A87 - 128
3X-RAY DIFFRACTION1A129 - 202
4X-RAY DIFFRACTION1A203 - 218
5X-RAY DIFFRACTION1A219 - 242
6X-RAY DIFFRACTION2B31 - 64
7X-RAY DIFFRACTION2B65 - 114
8X-RAY DIFFRACTION2B115 - 134
9X-RAY DIFFRACTION2B135 - 163
10X-RAY DIFFRACTION2B164 - 178
11X-RAY DIFFRACTION2B179 - 248

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