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- PDB-1ibd: X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29A -

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Basic information

Entry
Database: PDB / ID: 1ibd
TitleX-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29A
ComponentsCU,ZN SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / prokaryotic superoxide dismutase / subunit interaction
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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]
Similarity search - Component
Biological speciesPhotobacterium leiognathi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsStroppolo, M.E. / Pesce, A. / D'Orazio, M. / O'Neill, P. / Bordo, D. / Rosano, C. / Milani, M. / Battistoni, A. / Bolognesi, M. / Desideri, A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.
Authors: Stroppolo, M.E. / Pesce, A. / D'Orazio, M. / O'Neill, P. / Bordo, D. / Rosano, C. / Milani, M. / Battistoni, A. / Bolognesi, M. / Desideri, A.
History
DepositionMar 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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)15,9153
Polymers15,7861
Non-polymers1292
Water1,71195
1
A: CU,ZN SUPEROXIDE DISMUTASE
hetero molecules

A: CU,ZN SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8306
Polymers31,5722
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
Unit cell
Length a, b, c (Å)85.938, 85.938, 98.787
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

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Components

#1: Protein CU,ZN SUPEROXIDE DISMUTASE


Mass: 15785.800 Da / Num. of mol.: 1 / Mutation: V29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium leiognathi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00446, 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.: 95 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8k, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K
Crystal grow
*PLUS
Temperature: 100 K / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %PEG800011
20.1 M11NaCl
30.05 Msodium acetate11
410 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 2, 1999 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 8606 / Num. obs: 8606 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 21
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 91424

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: P.leiognathi Cu,Zn SOD wild type

Resolution: 2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 860 -random
Rwork0.214 ---
all-8606 --
obs-8606 90.5 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 2 95 1205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.26
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22 Å2

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