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- PDB-1mng: STRUCTURE-FUNCTION IN E. COLI IRON SUPEROXIDE DISMUTASE: COMPARIS... -

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Basic information

Entry
Database: PDB / ID: 1mng
TitleSTRUCTURE-FUNCTION IN E. COLI IRON SUPEROXIDE DISMUTASE: COMPARISONS WITH THE MANGANESE ENZYME FROM T. THERMOPHILUS
ComponentsMANGANESE SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE(SUPEROXIDE ACCEPTOR)
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
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 / Manganese/iron superoxide dismutase, C-terminal ...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
AZIDE ION / : / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLah, M.S. / Dixon, M. / Pattridge, K.A. / Stallings, W.C. / Fee, J.A. / Ludwig, M.L.
Citation
Journal: Biochemistry / Year: 1995
Title: Structure-function in Escherichia coli iron superoxide dismutase: comparisons with the manganese enzyme from Thermus thermophilus.
Authors: Lah, M.S. / Dixon, M.M. / Pattridge, K.A. / Stallings, W.C. / Fee, J.A. / Ludwig, M.L.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Manganese Superoxide Dismutase from Thermus Thermophilus. A Structural Model Refined at 1.8 Angstroms Resolution
Authors: Ludwig, M.L. / Metzger, A.L. / Pattridge, K.A. / Stallings, W.C.
#2: Journal: Molecular Biology of Free Radical Scavenging Systems
Year: 1992
Title: Iron and Manganese Superoxide Dismutases: Catalytic Inferences from the Structures
Authors: Stallings, W.C. / Bull, C. / Fee, J.A. / Lah, M.S. / Ludwig, M.L.
#3: Journal: Free Radical Res.Commun. / Year: 1991
Title: Structure-Function Relationships in Fe-and Mn-Superoxide Dismutases
Authors: Stallings, W.C. / Metzger, A.L. / Pattridge, K.A. / Fee, J.A. / Ludwig, M.L.
#4: Journal: J.Biol.Chem. / Year: 1985
Title: The Structure of Manganese Superoxide Dismutase from Thermus Thermophilus at 2.4 Angstroms Resolution
Authors: Stallings, W.C. / Pattridge, K.A. / Strong, R.K. / Ludwig, M.L.
#5: Journal: J.Biol.Chem. / Year: 1984
Title: Manganese and Iron Superoxide Dismutases are Structural Homologs
Authors: Stallings, W.C. / Pattridge, K.A. / Strong, R.K. / Ludwig, M.L.
History
DepositionJul 13, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 14, 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_alt_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.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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 650HELIX ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON THE ALGORITHM OF KABSCH AND SANDER, WITH THE ...HELIX ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON THE ALGORITHM OF KABSCH AND SANDER, WITH THE FOLLOWING EXCEPTIONS: HELICES START WITH THE FIRST RESIDUE HAVING A HELICAL HYDROGEN BOND; SUCCESSIVE 3/10 TURNS ARE GIVEN PRIORITY OVER SHORT 3/10 HELICES.

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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)46,4536
Polymers46,2592
Non-polymers1944
Water3,603200
1
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)92,90512
Polymers92,5174
Non-polymers3888
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7080 Å2
ΔGint-49 kcal/mol
Surface area32850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.800, 146.800, 55.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO A 3 / 2: CIS PROLINE - PRO A 18 / 3: CIS PROLINE - PRO B 3 / 4: CIS PROLINE - PRO B 18
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0569, -0.94416, 0.32454), (-0.94061, -0.05828, -0.33445), (0.33469, -0.32429, -0.88477)
Vector: 73.13657, 73.14556, -0.32487)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein MANGANESE SUPEROXIDE DISMUTASE


Mass: 23129.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P61503, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
25 mMphosphate1drop
440 %satammonium sulfate1reservoir
50.5 Mpotassium acid phosphate1reservoir
3ammonium sulfate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 52673 / Redundancy: 6.5 % / Rmerge(I) obs: 0.077

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→20 Å / σ(F): 0
Details: FOR ATOMS THAT ARE PRESENTED IN ALTERNATE CONFORMATIONS, THE ALTERNATE LOCATION INDICATOR *L* REPRESENTS THOSE ATOMS IN THE CONFORMATION WITH AZIDE LIGANDED AND *U* REPRESENTS THOSE ATOMS IN ...Details: FOR ATOMS THAT ARE PRESENTED IN ALTERNATE CONFORMATIONS, THE ALTERNATE LOCATION INDICATOR *L* REPRESENTS THOSE ATOMS IN THE CONFORMATION WITH AZIDE LIGANDED AND *U* REPRESENTS THOSE ATOMS IN THE CONFORMATION WITHOUT AZIDE LIGANDED.
RfactorNum. reflection
Rwork0.179 -
obs0.179 52673
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 8 200 3490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.984
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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