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- PDB-1vew: MANGANESE SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1vew
TitleMANGANESE SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI
ComponentsMANGANESE SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / MANGANESE ENZYME / METALLOPROTEIN / DNA BINDING
Function / homology
Function and homology information


cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress ...cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress / protein homodimerization activity / DNA binding / metal ion binding / cytoplasm / 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 / 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 / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / HYDROXIDE ION / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEdwards, R.A. / Baker, H.M. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1998
Title: Crystal structure of Escherichia coli manganese superoxide dismutase at 2.1-angstrom resolution.
Authors: Edwards, R.A. / Baker, H.M. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N.
History
DepositionJan 20, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: MANGANESE SUPEROXIDE DISMUTASE
D: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,27512
Polymers91,9884
Non-polymers2888
Water7,404411
1
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1386
Polymers45,9942
Non-polymers1444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area17710 Å2
MethodPISA
2
C: MANGANESE SUPEROXIDE DISMUTASE
D: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1386
Polymers45,9942
Non-polymers1444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.840, 108.910, 182.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.134086, 0.977846, 0.160742), (0.977948, 0.104362, 0.180905), (0.160122, 0.181454, -0.970276)10.109, -12.668, 22.894
2given(-0.079286, -0.99648, 0.027237), (-0.996167, 0.080214, 0.034875), (-0.036937, -0.024368, -0.99902)103.408, 51.431, 46.994
3given(-0.956616, -0.172522, -0.234782), (0.21721, -0.959375, -0.180053), (-0.194181, -0.223239, 0.955227)115.999, 41.21, 24.594

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Components

#1: Protein
MANGANESE SUPEROXIDE DISMUTASE / MNSOD / MNSD


Mass: 22996.877 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: AB2463/PDT1-5 / References: UniProt: P00448, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING DROP METHOD. THE HANGING DROPS WERE SUSPENDED OVER 0.75ML OF WELL SOLUTION (16-30% PEG6000 AND 0.05M BICINE TITRATED TO PH8.5) AND ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING DROP METHOD. THE HANGING DROPS WERE SUSPENDED OVER 0.75ML OF WELL SOLUTION (16-30% PEG6000 AND 0.05M BICINE TITRATED TO PH8.5) AND CONSISTED OF 2UL OF WELL SOLUTION AND 2UL OF PROTEIN SOLUTION (MNSOD AT 12MG/ML IN WATER)., vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
28-15 %PEG60001drop
30.025 Mbicine titrated1drop
416-30 %PEG60001reservoir
50.05 Mbicine titrated1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: 0.3MM DIAMETER COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 56890 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.056 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 0.7 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.191 / % possible all: 77
Reflection
*PLUS
Num. measured all: 215051 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 77 % / Rmerge(I) obs: 0.191

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MNG

1mng


Resolution: 2.1→50 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT CSDX-PROTGEO
RfactorNum. reflection% reflection
Rfree0.21 2874 5 %
Rwork0.188 --
all0.186 53872 -
obs0.186 53872 92 %
Solvent computationSolvent model: MOEWS AND KRETSINGER (J.MOL.BIOL.(1975)91, 201-228)
Bsol: 130 Å2 / ksol: 0.83 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 8 411 6951
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0167160.4
X-RAY DIFFRACTIONt_angle_deg1.290720.6
X-RAY DIFFRACTIONt_dihedral_angle_d15.638921.2
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0151800.65
X-RAY DIFFRACTIONt_gen_planes0.0169682.2
X-RAY DIFFRACTIONt_it1.667003.4
X-RAY DIFFRACTIONt_nbd0.11421572
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.61.2
X-RAY DIFFRACTIONt_plane_restr0.0162.2

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