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- PDB-1pzs: Crystal Structure of a Cu-Zn Superoxide Dismutase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 1pzs
TitleCrystal Structure of a Cu-Zn Superoxide Dismutase from Mycobacterium tuberculosis at 1.63 resolution
ComponentsSuperoxide dismutase [Cu-Zn]
Keywordsoxidoreductase / metal binding protein / Cu-protein / beta core / antioxidant / metal binding / greek key beta barrel
Function / homology
Function and homology information


: / response to host / symbiont-mediated detoxification of host-generated reactive oxygen species / symbiont defense to host-produced reactive oxygen species / Tolerance of reactive oxygen produced by macrophages / cell wall / response to hydroperoxide / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals ...: / response to host / symbiont-mediated detoxification of host-generated reactive oxygen species / symbiont defense to host-produced reactive oxygen species / Tolerance of reactive oxygen produced by macrophages / cell wall / response to hydroperoxide / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / cell redox homeostasis / peptidoglycan-based cell wall / response to oxidative stress / copper ion binding / extracellular region / plasma membrane
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn] / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsDjinovic-Carugo, K. / Spagnolo, L. / Toro, I.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Unique Features of the sodC-encoded Superoxide Dismutase from Mycobacterium tuberculosis, a Fully Functional Copper-containing Enzyme Lacking Zinc in the Active Site.
Authors: Spagnolo, L. / Toro, I. / D'Orazio, M. / O'Neill, P. / Pedersen, J.Z. / Carugo, O. / Rotilio, G. / Battistoni, A. / Djinovic-Carugo, K.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.6Nov 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: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7692
Polymers20,7061
Non-polymers641
Water4,540252
1
A: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5394
Polymers41,4122
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3270 Å2
ΔGint-14 kcal/mol
Surface area14050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.040, 58.420, 51.390
Angle α, β, γ (deg.)90.00, 126.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

DetailsThe biological assembly is a dimer generated by the two fold axis: -x, y, -z

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 20705.762 Da / Num. of mol.: 1 / Fragment: sequence database residues 33-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: SODC OR RV0432 OR MT0447 OR MTCY22G10.29 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): QC871
References: UniProt: P0A608, UniProt: P9WGE9*PLUS, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, Ammonium sulfate, zinc chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.634→27.95 Å / Num. all: 20248 / Num. obs: 20248 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.62 % / Biso Wilson estimate: 21.844 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.54
Reflection shellResolution: 1.634→1.8 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 5.17 / Num. unique all: 4640 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JCV.pdb

1jcv


Resolution: 1.63→27.95 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.561 / SU ML: 0.054 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19027 1013 5 %RANDOM
Rwork0.15029 ---
all0.15233 20248 --
obs0.15233 19233 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å21.19 Å2
2---0.52 Å20 Å2
3---1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.63→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 1 252 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211248
X-RAY DIFFRACTIONr_bond_other_d0.0050.021108
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.951695
X-RAY DIFFRACTIONr_angle_other_deg1.85832593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335170
X-RAY DIFFRACTIONr_chiral_restr0.0840.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021420
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02227
X-RAY DIFFRACTIONr_nbd_refined0.1920.2208
X-RAY DIFFRACTIONr_nbd_other0.2530.21242
X-RAY DIFFRACTIONr_nbtor_other0.0840.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.225
X-RAY DIFFRACTIONr_mcbond_it0.8311.5841
X-RAY DIFFRACTIONr_mcangle_it1.48421348
X-RAY DIFFRACTIONr_scbond_it2.1233407
X-RAY DIFFRACTIONr_scangle_it3.4754.5347
LS refinement shellResolution: 1.634→1.676 Å / Rfactor Rfree error: 0.087 / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.307 61
Rwork0.339 1146
obs-1207

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