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- PDB-2wwo: Yersinia pseudotuberculosis Superoxide Dismutase C -

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Basic information

Entry
Database: PDB / ID: 2wwo
TitleYersinia pseudotuberculosis Superoxide Dismutase C
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / METAL-BINDING
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / copper ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesYERSINIA PSEUDOTUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBasak, A.K. / Duffield, M.L. / Naylor, C.E. / Huyet, J. / Titball, R.W.
CitationJournal: To be Published
Title: Crystal Structure of the Yersinia Pseudotuberculosis Superoxide Dismutase (Sodc)
Authors: Huyet, J. / Naylor, C.E. / Titball, R.W. / Bullifent, H. / Walker, N. / Jones, H.E. / Duffied, M.L. / Basak, A.K.
History
DepositionOct 26, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionNov 3, 2010ID: 2WN0
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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: SUPEROXIDE DISMUTASE [CU-ZN]
B: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,58112
Polymers34,7442
Non-polymers83710
Water3,909217
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-27.2 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.546, 97.546, 81.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2035-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:18 OR RESSEQ 20:56 OR RESSEQ...
211CHAIN B AND (RESSEQ 7:18 OR RESSEQ 20:56 OR RESSEQ...

NCS oper: (Code: given
Matrix: (0.40081, 0.68064, 0.61326), (0.69647, -0.66125, 0.2787), (0.59521, 0.31541, -0.73908)
Vector: 30.46413, -0.22247, -70.51259)

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Components

#1: Protein SUPEROXIDE DISMUTASE [CU-ZN] / SUPEROXIDE DISMUTASE C


Mass: 17371.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: IP32953 / Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q66ED7, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE CONTAINS SIGNAL PEPTIDE NOT PRESENT IN MATURE PROTEIN

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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: 2.9 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES-NAOH, PH 6.5, 0.2M ZNSO4, 25% PEG-MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 5, 2008 / Details: MIRRORS
RadiationMonochromator: SILICON (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→84.5 Å / Num. obs: 17976 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ESO

1eso


Resolution: 2.4→48.773 Å / SU ML: 0.39 / σ(F): 1.54 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 916 5.1 %
Rwork0.1665 --
obs0.1685 17944 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.138 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 43.008 Å2
Baniso -1Baniso -2Baniso -3
1-5.7588 Å2-0 Å2-0 Å2
2--5.7588 Å2-0 Å2
3----11.5176 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 31 217 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062323
X-RAY DIFFRACTIONf_angle_d0.9923160
X-RAY DIFFRACTIONf_dihedral_angle_d16.587824
X-RAY DIFFRACTIONf_chiral_restr0.062351
X-RAY DIFFRACTIONf_plane_restr0.008421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1021X-RAY DIFFRACTIONPOSITIONAL
12B1021X-RAY DIFFRACTIONPOSITIONAL0.078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52650.25471380.19712366X-RAY DIFFRACTION100
2.5265-2.68480.21131280.17252412X-RAY DIFFRACTION100
2.6848-2.89210.23911350.17122408X-RAY DIFFRACTION100
2.8921-3.18310.24171160.17282434X-RAY DIFFRACTION100
3.1831-3.64360.19721530.16752386X-RAY DIFFRACTION100
3.6436-4.590.1691290.13352460X-RAY DIFFRACTION100
4.59-48.78320.1811170.15412562X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6769-0.122-0.04810.2477-0.75630.4480.19230.3494-0.1067-0.60040.1276-0.6179-0.1403-0.04260.00070.61470.0545-0.08530.4237-0.03090.312545.054616.9675-42.501
20.62270.2753-0.47220.1281-0.85311.7830.04030.34060.0183-0.3011-0.19390.03470.23950.1215-0.00010.48540.0956-0.06280.3456-0.02210.260446.098610.948-38.9866
30.62440.00220.20691.78090.27631.6379-0.03320.0747-0.1393-0.2277-0.1139-0.02410.40010.1285-00.37260.05390.00870.3152-0.0060.300449.44098.1425-31.3035
40.00940.14130.0377-0.04150.068-0.0035-0.25110.66320.2352-0.5787-0.1956-0.4564-0.5972-0.0658-0.0010.56660.082-0.02080.4112-0.01030.304149.9915.2563-43.0827
5-0.0266-0.34940.0324-0.01040.15950.27410.3099-0.67990.14130.7097-0.30490.13710.1214-0.0574-0.00220.4844-0.01510.10240.3144-0.020.424229.81678.919-6.2853
60.64110.5961-0.50731.0977-0.61681.57780.1282-0.06060.09120.2946-0.0690.3857-0.1227-0.1166-0.00040.27870.05430.07890.244-0.06280.380332.484813.7762-10.9156
70.6052-0.1319-0.1071.5601-0.28870.48770.02540.02220.00250.0933-0.07270.2424-0.2324-0.107200.32730.0080.01630.2821-0.0340.314138.193519.4975-14.9175
8-0.05410.0027-0.1472-0.0535-0.0725-0.03810.2323-1.05180.11020.8988-0.3499-0.0861-0.0633-0.080.00070.4692-0.04240.07880.31680.02770.360934.499112.5458-4.0566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 4:21
2X-RAY DIFFRACTION2CHAIN A AND RESID 22:75
3X-RAY DIFFRACTION3CHAIN A AND RESID 76:155
4X-RAY DIFFRACTION4CHAIN A AND RESID 156:161
5X-RAY DIFFRACTION5CHAIN B AND RESID 7:21
6X-RAY DIFFRACTION6CHAIN B AND RESID 22:75
7X-RAY DIFFRACTION7CHAIN B AND RESID 76:143
8X-RAY DIFFRACTION8CHAIN B AND RESID 156:161

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