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- PDB-1gv3: The 2.0 Angstrom resolution structure of the catalytic portion of... -

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Basic information

Entry
Database: PDB / ID: 1gv3
TitleThe 2.0 Angstrom resolution structure of the catalytic portion of a cyanobacterial membrane-bound manganese superoxide dismutase
ComponentsMANGANESE SUPEROXIDE DISMUTASE
KeywordsMANGANESE SUPEROXIDE DISMUTASE / ANABAENA PCC 7120
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / superoxide dismutase
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAtzenhofer, W. / Regelsberger, G. / Jacob, U. / Huber, R. / Peschek, G.A. / Obinger, C.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The 2.0A Resolution Structure of the Catalytic Portion of a Cyanobacterial Membrane-Bound Manganese Superoxide Dismutase
Authors: Atzenhofer, W. / Regelsberger, G. / Jacob, U. / Peschek, G.A. / Furtmuller, P. / Huber, R. / Obinger, C.
History
DepositionFeb 5, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 23, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.5Dec 13, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5364
Polymers56,4262
Non-polymers1102
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)151.320, 151.320, 69.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein MANGANESE SUPEROXIDE DISMUTASE


Mass: 28213.043 Da / Num. of mol.: 2
Fragment: HELICAL HAIRPIN, ALPHA/BETA DOMAIN, RESIDUES 30-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7120 / Plasmid: PET-3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Z0M1
#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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
32.0 Mammonium sulfate1reservoir
45 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.518
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2001
RadiationMonochromator: GRAPHIT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.518 Å / Relative weight: 1
ReflectionResolution: 2.03→30.57 Å / Num. obs: 35333 / % possible obs: 93.9 % / Redundancy: 2.5 %
Reflection
*PLUS
Num. measured all: 124807

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MNG

1mng


Resolution: 2→100 Å / Data cutoff high absF: 10000 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.211 --
Rwork0.188 --
obs0.188 33267 93.9 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.34 Å20 Å2
2--1.69 Å20 Å2
3----3.39 Å2
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 2 166 3608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.248
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.552.5
Refinement
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 30.57 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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