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- PDB-1gn6: G152A mutant of Mycobacterium tuberculosis iron-superoxide dismutase. -

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Basic information

Entry
Database: PDB / ID: 1gn6
TitleG152A mutant of Mycobacterium tuberculosis iron-superoxide dismutase.
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE
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 / SYNCHROTRON / OTHER / Resolution: 2.9 Å
AuthorsBunting, K.A. / Cooper, J.B. / Saward, S. / Erskine, P.T. / Badasso, M.O. / Wood, S.P. / Zhang, Y. / Young, D.B.
CitationJournal: FEBS Lett. / Year: 1996
Title: X-Ray Structure Analysis of an Engineered Fe-Superoxide Dismutase Gly-Ala Mutant with Significantly Reduced Stability to Denaturant
Authors: Cooper, J.B. / Saward, S. / Erskine, P.T. / Badasso, M.O. / Wood, S.P. / Zhang, Y. / Young, D.B.
History
DepositionOct 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,5238
Polymers92,3004
Non-polymers2234
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.700, 85.600, 66.700
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9035, -0.2983, -0.3076), (-0.2988, -0.9532, 0.0469), (-0.3072, 0.0495, -0.9503)25.709, 63.881, 97.462
2given(-0.9035, 0.3077, 0.2983), (0.3114, -0.007, 0.9503), (0.2944, 0.9515, -0.0895)-5.68, -17.208, 19.802
3given(-0.9999, -0.0101, 0.01), (-0.0096, -0.039, -0.9992), (0.0104, -0.9992, 0.0389)19.742, 82.887, 79.61

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Components

#1: Protein
SUPEROXIDE DISMUTASE


Mass: 23074.889 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: MYCOBACTERIUM VACCAE (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.: 360 / 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: 2.09 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 277 K / pH: 7
Details: 100MM TRIS-HCL PH 7.0, 25% PEG 6000, PROTEIN CONCENTRATION = 3 MG/ML, 4 DEGREES CENTIGRADE.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.6 / PH range high: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.0 mg/mlprotein1drop
225-31 %PEG60001reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.9→99 Å / Num. obs: 60000 / % possible obs: 88.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.154
Reflection
*PLUS
Num. obs: 14468

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Processing

Software
NameClassification
CCP4refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.9→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.169 --
obs-14468 88.2 %
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 4 360 6640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.011
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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