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- PDB-2aps: CU/ZN SUPEROXIDE DISMUTASE FROM ACTINOBACILLUS PLEUROPNEUMONIAE -

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Basic information

Entry
Database: PDB / ID: 2aps
TitleCU/ZN SUPEROXIDE DISMUTASE FROM ACTINOBACILLUS PLEUROPNEUMONIAE
ComponentsPROTEIN (CU,ZN SUPEROXIDE DISMUTASE)
KeywordsSUPEROXIDE DISMUTASE / SOD / WATER-MEDIATED DIMER / BETA BARREL
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 speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsForest, K.T. / Langford, P.R. / Kroll, J.S. / Getzoff, E.D.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Cu,Zn superoxide dismutase structure from a microbial pathogen establishes a class with a conserved dimer interface.
Authors: Forest, K.T. / Langford, P.R. / Kroll, J.S. / Getzoff, E.D.
History
DepositionFeb 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 25, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_sheet / 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_asym_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_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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CU,ZN SUPEROXIDE DISMUTASE)
B: PROTEIN (CU,ZN SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8948
Polymers34,5092
Non-polymers3856
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.050, 123.880, 107.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-300-

CU

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.859, 0.5063, -0.0765), (0.5015, 0.8016, -0.3255), (-0.1035, -0.318, -0.9424)
Vector: 25.492, 11.143, 102.938)

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Components

#1: Protein PROTEIN (CU,ZN SUPEROXIDE DISMUTASE) / SOD


Mass: 17254.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: EACH ACTIVE SITE CONTAINS ONE COPPER AND ONE ZINC.
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Cellular location: PERIPLASM / Gene: SODC / Plasmid: PJSK157 / Cellular location (production host): PERIPLASM / Gene (production host): SODC / Production host: Escherichia coli (E. coli) / Strain (production host): QC779 / References: UniProt: P24702, GenBank: 1438120
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCU 300 AND CU 500 FORM CRYSTAL CONTACTS. CU 300 LIES ON A SPECIAL POSITION. CU 402 AND CU 602 ARE ...CU 300 AND CU 500 FORM CRYSTAL CONTACTS. CU 300 LIES ON A SPECIAL POSITION. CU 402 AND CU 602 ARE IN ACTIVE SITES. BOTH ZINC IONS ARE IN ACTIVE SITES.
Sequence detailsTHERE IS NO LEADER PEPTIDE IN THE PURIFIED PROTEIN (23 RESIDUES ARE CLEAVED) AND THE FIRST 5 ...THERE IS NO LEADER PEPTIDE IN THE PURIFIED PROTEIN (23 RESIDUES ARE CLEAVED) AND THE FIRST 5 RESIDUES OF THE EXPRESSED (MATURE) PROTEIN HAVE APPARENTLY BEEN CLEAVED DURING PURIFICATION. RESIDUES 6-12 ARE PRESENT IN THE PROTEIN BUT NOT SEEN IN THE ELECTRON DENSITY.

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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: 2.8 Å3/Da / Density % sol: 42 % / Description: SEARCH MODEL WAS A DIMER.
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117.2 mg/mlprotein1drop
225 mM1reservoirNa2PO4
325 mM1reservoirK2PO4
450 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 30234 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.054 / Net I/σ(I): 28
Reflection shellResolution: 1.9→1.96 Å / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 13.7 / % possible all: 92
Reflection
*PLUS
Num. measured all: 106143 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YAI

1yai


Resolution: 1.9→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: CHAIN B IS MUCH MORE WELL-ORDERED THAN CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1534 5 %RANDOM
Rwork0.221 ---
obs-30219 98 %-
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-25.8 Å20 Å20 Å2
2--22.9 Å20 Å2
3---16.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 6 126 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d1.5
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.016
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.9
X-RAY DIFFRACTIONx_mcangle_it23.1
X-RAY DIFFRACTIONx_scbond_it23.1
X-RAY DIFFRACTIONx_scangle_it2.54.7
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.325 146 5 %
Rwork0.343 2549 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_SOD.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLTOPHCSDX_SOD.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 28685
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 0.016

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