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- PDB-2rgz: Ensemble refinement of the protein crystal structure of human hem... -

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Basic information

Entry
Database: PDB / ID: 2rgz
TitleEnsemble refinement of the protein crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / Ensemble Refinement / Refinement Methodology Development / Structural Genomics Medical Relevance / Structural Genomics Community Request / HO-2 / HEME Oxygenase / Endoplasmic reticulum / Iron / Metal-binding / Microsome / Structural Genomics / 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
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Multi-conformer re-refinement / 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
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
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 / pdbx_initial_refinement_model

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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)62,2164
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.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Number of models16

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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: 2.56 Å3/Da / Density % sol: 51.94 %
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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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
CNS1.1phasing
RefinementMethod to determine structure: Multi-conformer re-refinement
Starting model: PDB entry 2QPP

2qpp


Resolution: 2.61→39.02 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1772722.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2qpp and the first data set in the deposited structure factor file for 2qpp ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2qpp and the first data set in the deposited structure factor file for 2qpp along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1005 5.1 %RANDOM
Rwork0.161 ---
obs-19515 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.313 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.61→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 86 83 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.22.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.61-2.770.3731544.90.31829770.033238313196.7
2.77-2.990.2961755.50.19430300.0223211320599.8
2.99-3.290.2881665.10.16930630.0223232322999.9
3.29-3.760.2671765.40.17330800.023258325699.9
3.76-4.740.2031815.50.12930910.0153291327299.4
4.74-39.020.2411534.50.15132690.0193426342299.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hemeFE+3.par

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