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- PDB-2wwn: Yersinia pseudotuberculosis Superoxide Dismutase C with bound Azide -

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Basic information

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


superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding / extracellular space
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 / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
AZIDE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesYERSINIA PSEUDOTUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: 2WN1
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_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.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_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_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

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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)35,48112
Polymers34,7442
Non-polymers73710
Water2,378132
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-111.6 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.561, 96.561, 81.716
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-2017-

HOH

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

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:11 OR RESSEQ 13:18 OR RESSEQ...
211CHAIN B AND (RESSEQ 7:11 OR RESSEQ 13:18 OR RESSEQ...

NCS oper: (Code: given
Matrix: (0.40183, -0.67247, -0.62154), (-0.68661, -0.67036, 0.2814), (-0.60589, 0.31368, -0.73109)
Vector: 13.3626, 6.77134, 23.20671)

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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-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 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, 10MM NA AZIDE

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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: 2.6→50 Å / Num. obs: 13914 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.74 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % 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: 2.6→41.812 Å / SU ML: 0.46 / σ(F): 1.95 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 698 5 %
Rwork0.1859 --
obs0.1882 13886 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.741 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-5.8506 Å2-0 Å2-0 Å2
2--5.8506 Å2-0 Å2
3----11.7011 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 25 132 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042285
X-RAY DIFFRACTIONf_angle_d0.873115
X-RAY DIFFRACTIONf_dihedral_angle_d14.771791
X-RAY DIFFRACTIONf_chiral_restr0.052350
X-RAY DIFFRACTIONf_plane_restr0.008417
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A945X-RAY DIFFRACTIONPOSITIONAL
12B945X-RAY DIFFRACTIONPOSITIONAL0.075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80080.25281340.21752597X-RAY DIFFRACTION100
2.8008-3.08250.3011370.20062604X-RAY DIFFRACTION100
3.0825-3.52840.26121650.19442583X-RAY DIFFRACTION100
3.5284-4.44460.19951350.16372630X-RAY DIFFRACTION100
4.4446-41.81770.19821270.16632774X-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)
11.0339-0.52570.09761.6162-0.1612.65150.0381-0.18790.05420.258-0.21020.0401-0.15440.0430.00020.4326-0.08630.03610.3802-0.02870.270447.1062-10.38398.2765
21.5903-0.5099-0.48771.58120.47522.3712-0.00350.001-0.0541-0.2231-0.16990.52030.16-0.212700.3644-0.0527-0.06520.318-0.05320.412833.8735-16.4601-14.6077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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