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- PDB-6bej: Crystal structure of manganese superoxide dismutase from Xanthomo... -

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Basic information

Entry
Database: PDB / ID: 6bej
TitleCrystal structure of manganese superoxide dismutase from Xanthomonas citri
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / Enzyme / superoxide dismutase
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / peroxidase activity / metal ion binding
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase / Superoxide dismutase
Similarity search - Component
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.894 Å
AuthorsGoto, L.S. / Alexandrino, A.V. / Pereira, C.M. / Mendoca, D.C. / Leonardo, D.A. / Pereira, H.M. / Garratt, R.C. / Novo-Mansur, M.T.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Capes23038.006942/2011-31 Brazil
Sao Paulo Research Foundation (FAPESP)2007/50910-2 Brazil
CitationJournal: PLoS ONE / Year: 2019
Title: Structural characterization of a pathogenicity-related superoxide dismutase codified by a probably essential gene in Xanthomonas citri subsp. citri.
Authors: Cabrejos, D.A.L. / Alexandrino, A.V. / Pereira, C.M. / Mendonca, D.C. / Pereira, H.D. / Novo-Mansur, M.T.M. / Garratt, R.C. / Goto, L.S.
History
DepositionOct 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Superoxide dismutase
A: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5974
Polymers45,4872
Non-polymers1102
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.670, 72.466, 87.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 66 or resid 68...
21(chain E and (resid 2 through 49 or (resid 50...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASNASN(chain A and (resid 2 through 66 or resid 68...AB2 - 662 - 66
12GLNGLNPROPRO(chain A and (resid 2 through 66 or resid 68...AB68 - 9668 - 96
13LYSLYSLYSLYS(chain A and (resid 2 through 66 or resid 68...AB9797
14ALAALAILEILE(chain A and (resid 2 through 66 or resid 68...AB2 - 2022 - 202
15ALAALAILEILE(chain A and (resid 2 through 66 or resid 68...AB2 - 2022 - 202
16ALAALAILEILE(chain A and (resid 2 through 66 or resid 68...AB2 - 2022 - 202
17ALAALAILEILE(chain A and (resid 2 through 66 or resid 68...AB2 - 2022 - 202
21ALAALAALAALA(chain E and (resid 2 through 49 or (resid 50...EA2 - 492 - 49
22ASPASPASPASP(chain E and (resid 2 through 49 or (resid 50...EA5050
23ALAALAILEILE(chain E and (resid 2 through 49 or (resid 50...EA2 - 2022 - 202
24ALAALAILEILE(chain E and (resid 2 through 49 or (resid 50...EA2 - 2022 - 202
25ALAALAILEILE(chain E and (resid 2 through 49 or (resid 50...EA2 - 2022 - 202
26ALAALAILEILE(chain E and (resid 2 through 49 or (resid 50...EA2 - 2022 - 202

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Components

#1: Protein Superoxide dismutase /


Mass: 22743.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Gene: IB69_010705 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): DE3
References: UniProt: A0A1V9H1W3, UniProt: Q8PJZ1*PLUS, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1 M Bis Tris pH 6.1, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 17, 2015
RadiationMonochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→27.982 Å / Num. obs: 30880 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.601 % / Biso Wilson estimate: 27.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.062 / Χ2: 0.922 / Net I/σ(I): 17.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.89-2.015.3510.4533.5747270.9430.595.2
2.01-2.155.6310.2576.3347000.9790.28399.6
2.15-2.325.5930.1789.3843310.9890.19799.2
2.32-2.545.7540.1212.8939670.9930.13397.9
2.54-2.835.7520.08118.3536030.9970.08998.2
2.83-3.275.7340.05726.1332580.9970.06398.8
3.27-3.995.5650.0437.4627720.9980.04499.6
3.99-5.585.5730.03143.6322130.9980.03499.4
5.58-27.9825.3360.02744.3913090.9990.0397.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCV

2rcv


Resolution: 1.894→27.982 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.12
RfactorNum. reflection% reflection
Rfree0.251 1544 5 %
Rwork0.2027 --
obs0.2052 30866 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.4 Å2 / Biso mean: 38.1469 Å2 / Biso min: 15.01 Å2
Refinement stepCycle: final / Resolution: 1.894→27.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 2 304 3450
Biso mean--22.61 40.03 -
Num. residues----402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043250
X-RAY DIFFRACTIONf_angle_d0.6884445
X-RAY DIFFRACTIONf_chiral_restr0.044469
X-RAY DIFFRACTIONf_plane_restr0.005588
X-RAY DIFFRACTIONf_dihedral_angle_d14.3911885
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1789X-RAY DIFFRACTION7.571TORSIONAL
12E1789X-RAY DIFFRACTION7.571TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8939-1.9550.34551280.29152446257492
1.955-2.02480.28251410.242726602801100
2.0248-2.10590.31241390.23926572796100
2.1059-2.20170.2911400.22626542794100
2.2017-2.31770.30531400.23522656279699
2.3177-2.46280.3261380.22722624276298
2.4628-2.65290.29581400.22462659279998
2.6529-2.91960.26281410.21342668280998
2.9196-3.34150.26041420.20152696283899
3.3415-4.20760.20321440.17552740288499
4.2076-27.98520.20891510.17862862301399
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)
12.5466-0.08020.22551.78130.07545.2856-0.112-0.0638-0.2369-0.07270.00680.21240.2479-0.28590.08690.1932-0.00840.03660.13240.02080.25014.678668.354822.3085
23.3258-1.0580.14262.7998-0.09993.19060.11210.21510.2535-0.2845-0.06690.2988-0.3098-0.3917-0.02910.24120.0383-0.00910.1610.02720.2516.117677.28299.754
31.4164-0.91871.3894.7827-0.75321.3759-0.13840.0927-0.4041-0.3666-0.1163-0.1530.56690.8687-0.06410.57170.27480.12580.4446-0.01380.318232.302657.92085.9332
44.1009-0.10120.46166.448-1.69563.8225-0.1597-0.04240.1563-0.35290.1339-0.1839-0.07680.93730.35050.2458-0.02570.0120.3726-0.01680.184631.495773.39032.6233
52.5597-0.26041.49312.0717-0.54712.7556-0.0196-0.09830.422-0.037-0.1899-0.7485-0.79741.38120.16070.5672-0.31230.01670.87740.02980.505740.115582.5568.0102
64.4808-1.04480.56293.86670.66074.6748-0.0964-0.35460.1909-0.0604-0.0644-0.3305-0.3261.0740.12490.2143-0.04730.00320.4698-0.01830.2133.681874.125110.6533
70.3979-0.17090.35120.5684-0.08790.5459-0.1065-0.283-0.1599-0.01-0.1155-0.36220.13470.3156-0.50640.53570.55590.07561.24390.11920.499643.54957.354526.7805
83.2993-1.57982.00722.65720.15771.8947-0.3403-0.3452-0.43580.64820.22830.04930.24740.71680.03250.34830.21850.03470.62310.0610.260431.199164.363726.6855
92.723-0.90061.40831.6854-0.77222.3131-0.1084-0.50850.14660.0667-0.2105-0.20050.22640.89540.24770.28240.06390.06290.5780.01080.197730.950567.17519.9057
102.35-0.1682-1.30090.1370.10610.7224-0.4221-0.6021-0.66850.28370.2758-0.43940.43360.3460.08330.48970.27280.0760.46480.09310.41430.189955.326221.2437
110.1802-0.0118-0.09780.00120.00780.0531-0.01960.16770.1335-0.0137-0.1161-0.12630.0810.49490.17290.36620.27580.09511.33080.28120.446847.195662.905320.43
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 2 through 97 )E2 - 97
2X-RAY DIFFRACTION2chain 'E' and (resid 98 through 202 )E98 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 30 )A2 - 30
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 43 )A31 - 43
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 64 )A44 - 64
6X-RAY DIFFRACTION6chain 'A' and (resid 65 through 87 )A65 - 87
7X-RAY DIFFRACTION7chain 'A' and (resid 88 through 110 )A88 - 110
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 135 )A111 - 135
9X-RAY DIFFRACTION9chain 'A' and (resid 136 through 177 )A136 - 177
10X-RAY DIFFRACTION10chain 'A' and (resid 178 through 190 )A178 - 190
11X-RAY DIFFRACTION11chain 'A' and (resid 191 through 202 )A191 - 202

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