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- PDB-1eso: MONOMERIC CU,ZN SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1eso
TitleMONOMERIC CU,ZN SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI
ComponentsCU, ZN SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / CU / ZN SUPEROXIDE DISMUTASE / MONOMERIC SUPEROXIDE DISMUTASE / COPPER ENZYMES / ENZYME EVOLUTION / X-RAY CRYSTAL STRUCTURE
Function / homology
Function and homology information


superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding / zinc ion binding / metal ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn] / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPesce, A. / Capasso, C. / Battistoni, A. / Folcarelli, S. / Rotilio, G. / Desideri, A. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Unique structural features of the monomeric Cu,Zn superoxide dismutase from Escherichia coli, revealed by X-ray crystallography.
Authors: Pesce, A. / Capasso, C. / Battistoni, A. / Folcarelli, S. / Rotilio, G. / Desideri, A. / Bolognesi, M.
History
DepositionJun 27, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / software / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _software.name / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CU, ZN SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8903
Polymers15,7611
Non-polymers1292
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.000, 52.400, 43.200
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CU, ZN SUPEROXIDE DISMUTASE / SOD


Mass: 15760.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BMH 71-18 / Cellular location: PERIPLASM / Gene: SODC / Production host: Escherichia coli (E. coli)
References: UniProt: P53635, UniProt: P0AGD1*PLUS, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS, PH 8.5
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
230 %(w/v)PEG40001reservoir
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 7, 1996 / Details: PINHOLE COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→26.3 Å / Num. obs: 9044 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.07 / % possible all: 87
Reflection
*PLUS
Num. measured all: 28077

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
AMoREphasing
TNT5Brefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY SIRAS IN THE DEPOSITORS' LAB

Resolution: 2→26 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT: ENGH-HUBER
RfactorNum. reflection% reflection
Rfree0.26 433 5 %
Rwork0.168 --
all-8624 -
obs-9057 96.4 %
Solvent computationSolvent model: TNT / Bsol: 103.3 Å2 / ksol: 0.76 e/Å3
Refinement stepCycle: LAST / Resolution: 2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 2 75 1180
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01811256
X-RAY DIFFRACTIONt_angle_deg2.78151010.5
X-RAY DIFFRACTIONt_dihedral_angle_d19.366950
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018328.5
X-RAY DIFFRACTIONt_gen_planes0.01916528
X-RAY DIFFRACTIONt_it4.711257
X-RAY DIFFRACTIONt_nbd0.062130.062
Software
*PLUS
Name: TNT / Version: 5B / Classification: refinement
Refinement
*PLUS
Num. reflection all: 9057 / Num. reflection obs: 8624 / Rfactor all: 0.168 / Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.360
X-RAY DIFFRACTIONt_planar_d0.0188.5
X-RAY DIFFRACTIONt_plane_restr0.01928

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