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- PDB-6jov: Crystal structure of a hypothetical Fe Superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 6jov
TitleCrystal structure of a hypothetical Fe Superoxide dismutase
ComponentsFe-Superoxide dismutase
KeywordsMETAL BINDING PROTEIN / Superoxide dismutase / Fe / metalloenzyme / Reactive oxygen species / antioxidant
Function / homology: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsBose, S. / Purushothaman, S.S. / Subramanian, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India) India
CitationJournal: To Be Published
Title: Crystal structure of a hypothetical Fe Superoxide dismutase
Authors: Ashok, A. / Bose, S. / Jain, C. / Purushothaman, S.S. / Subramanian, R.
History
DepositionMar 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe-Superoxide dismutase
B: Fe-Superoxide dismutase
C: Fe-Superoxide dismutase
D: Fe-Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,24642
Polymers98,1504
Non-polymers4,09638
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.018, 55.088, 74.623
Angle α, β, γ (deg.)82.28, 89.61, 68.49
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Fe-Superoxide dismutase


Mass: 24537.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: superoxide dismutase

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Non-polymers , 7 types, 389 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris 8.0 and 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→45.33 Å / Num. obs: 58082 / % possible obs: 97.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.04 / Rrim(I) all: 0.08 / Rsym value: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.31 / Num. unique obs: 3866 / CC1/2: 0.91 / Rpim(I) all: 0.19 / Rrim(I) all: 0.37 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MY6

1my6


Resolution: 1.941→44.895 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 2892 5.01 %
Rwork0.1814 --
obs0.1837 57721 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.941→44.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 260 351 6838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066653
X-RAY DIFFRACTIONf_angle_d0.8378977
X-RAY DIFFRACTIONf_dihedral_angle_d5.9724135
X-RAY DIFFRACTIONf_chiral_restr0.049955
X-RAY DIFFRACTIONf_plane_restr0.0061134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9409-1.97270.26221330.20772533X-RAY DIFFRACTION93
1.9727-2.00670.25481350.20092546X-RAY DIFFRACTION96
2.0067-2.04320.24811380.19392630X-RAY DIFFRACTION97
2.0432-2.08250.25191330.20232539X-RAY DIFFRACTION95
2.0825-2.1250.23311400.18142650X-RAY DIFFRACTION97
2.125-2.17120.22661360.17922571X-RAY DIFFRACTION97
2.1712-2.22170.25851390.17932653X-RAY DIFFRACTION97
2.2217-2.27730.25161350.19232534X-RAY DIFFRACTION94
2.2773-2.33880.24241380.18172630X-RAY DIFFRACTION97
2.3388-2.40760.24281390.18352646X-RAY DIFFRACTION97
2.4076-2.48530.24511380.1852612X-RAY DIFFRACTION98
2.4853-2.57420.25361380.18432621X-RAY DIFFRACTION97
2.5742-2.67720.22651380.18122613X-RAY DIFFRACTION97
2.6772-2.7990.21871400.17722669X-RAY DIFFRACTION98
2.799-2.94660.22061390.17452626X-RAY DIFFRACTION98
2.9466-3.13120.21921390.18352634X-RAY DIFFRACTION98
3.1312-3.37280.2361390.18112631X-RAY DIFFRACTION98
3.3728-3.71210.20521380.17112616X-RAY DIFFRACTION97
3.7121-4.24890.21441390.16612625X-RAY DIFFRACTION97
4.2489-5.35180.191390.17362633X-RAY DIFFRACTION98
5.3518-44.90720.23081390.19842617X-RAY DIFFRACTION97

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