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- PDB-2a03: Superoxide dismutase protein from plasmodium berghei -

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Basic information

Entry
Database: PDB / ID: 2a03
TitleSuperoxide dismutase protein from plasmodium berghei
ComponentsFe-superoxide dismutase homolog
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology: / :
Function and homology information
Biological speciesPlasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsHolmes, M.A. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be published
Title: Hypothetical protein from plasmodium berghei
Authors: Holmes, M.A. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionJun 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.description / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE IDENTITY OF THE METAL IONS AT SITES 200 AND 300 IS UNCERTAIN. THIS MODEL CONTAINS MN ...HETEROGEN THE IDENTITY OF THE METAL IONS AT SITES 200 AND 300 IS UNCERTAIN. THIS MODEL CONTAINS MN IONS AT THESE SITES, BUT X-RAY FLUORESCENCE SCANS INDICATE THAT SOME FRACTION MAY INSTEAD BE FE IONS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe-superoxide dismutase homolog
B: Fe-superoxide dismutase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4285
Polymers47,2532
Non-polymers1753
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-29 kcal/mol
Surface area17450 Å2
MethodPISA
2
A: Fe-superoxide dismutase homolog
B: Fe-superoxide dismutase homolog
hetero molecules

A: Fe-superoxide dismutase homolog
B: Fe-superoxide dismutase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,85710
Polymers94,5064
Non-polymers3516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area5230 Å2
ΔGint-92 kcal/mol
Surface area33530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.111, 105.111, 207.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Fe-superoxide dismutase homolog


Mass: 23626.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: PB000490.02.0 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q4YW77, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.4 ul protein 20 mg/ml, 0.4 ul crystallization buffer, 100mM Zn acetate, 14% PEG 8000, 80mM Na citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 29521 / % possible obs: 98.7 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.704
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID
2.33-2.4186.80.4652.95225051
2.41-2.5199.40.4464.50529341
2.51-2.6299.90.4056.17829171
2.62-2.761000.3278.67429401
2.76-2.941000.19614.01629371
2.94-3.161000.1221.23329621
3.16-3.481000.08330.55129801
3.48-3.981000.05843.30430041
3.98-5.021000.04756.98330591
5.02-501000.03459.57832831

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Phasing

Phasing MRRfactor: 0.552 / Cor.coef. Fo:Fc: 0.35
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
EPMR2.5phasing
PDB_EXTRACT1.6data extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005 24/04/2001refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ISC

1isc


Resolution: 2.33→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 1493 5.081 %random
Rwork0.1707 ---
obs-29383 98.963 %-
Solvent computationSolvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.207 Å2
Baniso -1Baniso -2Baniso -3
1-1.332 Å20.666 Å20 Å2
2--1.332 Å20 Å2
3----1.997 Å2
Refinement stepCycle: LAST / Resolution: 2.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 3 256 3392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213260
X-RAY DIFFRACTIONr_bond_other_d0.0010.022732
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.8994447
X-RAY DIFFRACTIONr_angle_other_deg0.70736391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82625.412170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66215495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.173154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023696
X-RAY DIFFRACTIONr_gen_planes_other00.02668
X-RAY DIFFRACTIONr_nbd_refined0.2080.3757
X-RAY DIFFRACTIONr_nbd_other0.180.32668
X-RAY DIFFRACTIONr_nbtor_refined0.190.51610
X-RAY DIFFRACTIONr_nbtor_other0.0890.51572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5346
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3080.514
X-RAY DIFFRACTIONr_mcbond_it0.89622527
X-RAY DIFFRACTIONr_mcbond_other0.1672807
X-RAY DIFFRACTIONr_mcangle_it1.17533134
X-RAY DIFFRACTIONr_mcangle_other0.51332734
X-RAY DIFFRACTIONr_scbond_it1.88841601
X-RAY DIFFRACTIONr_scbond_other0.5742680
X-RAY DIFFRACTIONr_scangle_it2.64161313
X-RAY DIFFRACTIONr_scangle_other1.09163657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.3910.3321070.2241737211087.393
2.391-2.4560.288910.2111937206498.256
2.456-2.5260.251070.2081917202699.901
2.526-2.6020.2631030.1881844194999.897
2.602-2.6860.2241110.18718021913100
2.686-2.7780.1971070.17417481855100
2.778-2.8810.174830.16616871770100
2.881-2.9960.172940.16316521746100
2.996-3.1260.199950.16815521647100
3.126-3.2750.207800.17415231603100
3.275-3.4470.206540.16914631517100
3.447-3.6490.216850.1811378146499.932
3.649-3.8920.216700.161303137499.927
3.892-4.190.203690.14212131282100
4.19-4.570.13510.13911541205100
4.57-5.0770.203400.14410481088100
5.077-5.80.173440.184954998100
5.8-6.9590.212500.189813863100
6.959-9.2950.139340.159678712100
9.295-200.147180.201487505100
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)
11.172-0.0630.2620.619-0.31412.0785-0.0366-0.04680.16080.0235-0.00860.0157-0.10940.01840.04530.00160.022-0.00030.0132-0.0133-0.002330.2730.581122.267
21.5276-0.5094-0.05640.97660.24354.09930.07950.14120.18450.01-0.0379-0.1936-0.09090.2673-0.04160.03530.04320.0080.00430.0161-0.021328.50529.524136.478
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 197 / Label seq-ID: 9 - 205

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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