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- PDB-1gn2: S123C mutant of the iron-superoxide dismutase from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 1gn2
TitleS123C mutant of the iron-superoxide dismutase from Mycobacterium tuberculosis.
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / IRON
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 / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBunting, K.A. / Cooper, J.B. / Tickle, I.J. / Young, D.B.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2002
Title: Engineering of an Intersubunit Disulfide Bridge in the Iron-Superoxide Dismutase of Mycobacterium Tuberculosis.
Authors: Bunting, K.A. / Cooper, J.B. / Tickle, I.J. / Young, D.B.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Engineering a Change in Metal-Ion Specificity of the Iron-Dependent Superoxide Dismutase from Mycobacterium Tuberculosis-- X-Ray Structure Analysis of Site-Directed Mutants
Authors: Bunting, K. / Cooper, J.B. / Badasso, M.O. / Tickle, I.J. / Newton, M. / Wood, S.P. / Zhang, Y. / Young, D.
History
DepositionOct 2, 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: SUPEROXIDE DISMUTASE
F: SUPEROXIDE DISMUTASE
G: SUPEROXIDE DISMUTASE
H: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,06216
Polymers184,6158
Non-polymers4478
Water00
1
A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
C: SUPEROXIDE DISMUTASE
D: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5318
Polymers92,3084
Non-polymers2234
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-103 kcal/mol
Surface area34310 Å2
MethodPQS
2
E: SUPEROXIDE DISMUTASE
F: SUPEROXIDE DISMUTASE
G: SUPEROXIDE DISMUTASE
H: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5318
Polymers92,3084
Non-polymers2234
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14600 Å2
ΔGint-101.3 kcal/mol
Surface area34480 Å2
MethodPQS
Unit cell
Length a, b, c (Å)103.080, 106.330, 76.100
Angle α, β, γ (deg.)90.00, 92.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6653, -0.5911, 0.456), (-0.5897, 0.0415, -0.8065), (0.4579, -0.8055, -0.3762)139.338, 30.107, -63.081
2given(-0.3552, -0.3094, -0.8821), (-0.3224, -0.8452, 0.4263), (-0.8774, 0.4358, 0.2004)137.13699, -51.96, 119.249
3given(0.0117, 0.9099, 0.4146), (0.905, -0.186, 0.3825), (0.4252, 0.3708, -0.8257)134.83701, -148.849, -3.33
4given(-0.9754, 0.21, -0.067), (-0.189, -0.9533, -0.2354), (-0.1133, -0.2169, 0.9696)56.288, 50.387, 42.562
5given(0.4962, 0.6344, -0.5928), (0.5768, 0.2693, 0.7711), (0.6488, -0.7246, -0.2323)-69.592, 10.823, -41.382
6given(0.3303, 0.1043, 0.9381), (0.5749, 0.766, -0.2876), (-0.7486, 0.6343, 0.1931)-95.46, 46.56, 154.66901
7given(0.1546, -0.9478, -0.2787), (-0.9651, -0.0846, -0.2477), (0.2112, 0.3073, -0.9279)-106.554, 167.285, 57.188

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Components

#1: Protein
SUPEROXIDE DISMUTASE


Mass: 23076.926 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: Fe
Compound detailsENGINEERED MUTATION: OTHER_DETAILS: DISULPHIDE BRIDGE BETWEEN CYS 123 OF NCS RELATED SUBUNITS.
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: 2.26 Å3/Da / Density % sol: 39.7 %
Crystal growpH: 7
Details: 100MM TRIS-HCL PH 7.0, 25% PEG 6000, PROTEIN CONCENTRATION = 3 MG/ML.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.0 mg/mlprotein1drop
2100 mMTris1reservoirpH7.0
325 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→24 Å / Num. obs: 15208 / % possible obs: 67.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 3.5
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.6 / % possible all: 67.7
Reflection
*PLUS
Lowest resolution: 24 Å

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Processing

Software
NameClassification
CCP4refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IDS

1ids


Resolution: 3.4→21 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: INDIVIDUAL B-FACTORS NO REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 750 5 %RANDOM
Rwork0.249 ---
obs-15192 67.5 %-
Refinement stepCycle: LAST / Resolution: 3.4→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12544 0 8 0 12552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.027
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_restr0.009
X-RAY DIFFRACTIONp_chiral_restr0.015
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
Lowest resolution: 21 Å / Rfactor obs: 0.249 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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