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- PDB-2aqn: CU/ZN superoxide dismutase from neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 2aqn
TitleCU/ZN superoxide dismutase from neisseria meningitidis
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / superoxide dismutase / neisseria meningitidis.
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / periplasmic space / 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
COPPER (II) ION / COPPER (I) ION / Superoxide dismutase [Cu-Zn] / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDiDonato, M. / Kassmann, C.J. / Bruns, C.K. / Cabelli, D.E. / Cao, Z. / Tabatabai, L.B. / Kroll, J.S. / Getzoff, E.D.
CitationJournal: To be Published
Title: CU/ZN superoxide dismutase from neisseria meningitidis
Authors: DiDonato, M. / Kassmann, C.J. / Bruns, C.K. / Cabelli, D.E. / Cao, Z. / Tabatabai, L.B. / Kroll, J.S. / Getzoff, E.D.
History
DepositionAug 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: 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_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_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

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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]
C: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77212
Polymers52,1623
Non-polymers6109
Water9,548530
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1928
Polymers34,7752
Non-polymers4186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-29 kcal/mol
Surface area13620 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
hetero molecules

C: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1608
Polymers34,7752
Non-polymers3856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
3
C: Superoxide dismutase [Cu-Zn]
hetero molecules

C: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,54424
Polymers104,3246
Non-polymers1,22018
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11320 Å2
ΔGint-118 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.791, 64.592, 82.730
Angle α, β, γ (deg.)90.00, 125.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-301-

CU

21A-850-

HOH

31B-831-

HOH

41B-874-

HOH

51B-948-

HOH

61C-825-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 17387.371 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: sodC / Production host: Escherichia coli (E. coli)
References: UniProt: Q59623, UniProt: P57005*PLUS, superoxide dismutase

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Non-polymers , 5 types, 539 molecules

#2: Chemical ChemComp-CU1 / COPPER (I) ION


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


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: AmSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Date: Feb 7, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 80120 / Num. obs: 80120 / % possible obs: 95.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 14.1
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.252 / % possible all: 93.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2APS

2aps


Resolution: 1.4→30 Å / Num. parameters: 36222 / Num. restraintsaints: 43967 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT DECREASED R BY 5.24 %
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 4009 5 %RANDOM
Rwork0.1285 ---
obs0.1285 80120 95.7 %-
all-80120 --
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 3303 / Occupancy sum non hydrogen: 3994.32
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 13 530 4025
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0299
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.079

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