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- PDB-1ids: X-RAY STRUCTURE ANALYSIS OF THE IRON-DEPENDENT SUPEROXIDE DISMUTA... -

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Entry
Database: PDB / ID: 1ids
TitleX-RAY STRUCTURE ANALYSIS OF THE IRON-DEPENDENT SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS AT 2.0 ANGSTROMS RESOLUTIONS REVEALS NOVEL DIMER-DIMER INTERACTIONS
ComponentsIRON SUPEROXIDE DISMUTASE
KeywordsSUPEROXIDE DISMUTASE
Function / homology
Function and homology information


Tolerance of reactive oxygen produced by macrophages / detoxification / superoxide dismutase / superoxide dismutase activity / manganese ion binding / response to oxidative stress / periplasmic space / iron ion binding / extracellular region / plasma membrane / cytosol
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 ...: / 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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Fe] / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsCooper, J.B. / Mcintyre, K. / Wood, S.P. / Zhang, Y. / Young, D.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: X-ray structure analysis of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis at 2.0 Angstroms resolution reveals novel dimer-dimer interactions.
Authors: Cooper, J.B. / McIntyre, K. / Badasso, M.O. / Wood, S.P. / Zhang, Y. / Garbe, T.R. / Young, D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallisation and Preliminary X-Ray Analysis of the Iron-Dependent Superoxide Dismutase from Mycobacterium Tuberculosis
Authors: Cooper, J.B. / Driessen, H.P.C. / Wood, S.P. / Zhang, Y. / Young, D.
History
DepositionSep 29, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET SHEET_ID: EA, SHEET IN A SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: EB, SHEET IN ...SHEET SHEET SHEET_ID: EA, SHEET IN A SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: EB, SHEET IN B SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: EC, SHEET IN C SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: ED, SHEET IN D SUBUNIT. N-CENTERED OVERHAND TOPOLOGY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IRON SUPEROXIDE DISMUTASE
B: IRON SUPEROXIDE DISMUTASE
C: IRON SUPEROXIDE DISMUTASE
D: IRON SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4678
Polymers92,2434
Non-polymers2234
Water11,818656
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-87 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.650, 85.400, 66.350
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 18 / 2: CIS PROLINE - PRO B 18 / 3: CIS PROLINE - PRO C 18 / 4: CIS PROLINE - PRO D 18

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Components

#1: Protein
IRON SUPEROXIDE DISMUTASE


Mass: 23060.861 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
References: UniProt: P17670, UniProt: P9WGE7*PLUS, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHETATMS 1001-1004 ARE PUTATIVE OH(-) IONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlenzyme1drop
223 %(w/v)PEG60001reservoir
30.1 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 40396 / % possible obs: 80.4 %
Reflection
*PLUS
Highest resolution: 2 Å

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementHighest resolution: 2 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.167 40396 80.4 %
Displacement parametersBiso mean: 20.61 Å2
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 4 656 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0050.02
X-RAY DIFFRACTIONp_angle_d0.0190.04
X-RAY DIFFRACTIONp_planar_d0.0080.017
X-RAY DIFFRACTIONp_multtor_nbd0.030.05
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection all: 40396 / Rfactor all: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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