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- PDB-1en5: CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DI... -

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Basic information

Entry
Database: PDB / ID: 1en5
TitleCRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Y34F MUTANT
ComponentsMANGANESE SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / proton shuttle / Y34F / mutant / manganese superoxide dismutase
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 / 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 [Mn]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsEdwards, R.A. / Whittaker, M.M. / Baker, E.N. / Whittaker, J.W. / Jameson, G.B.
Citation
Journal: Biochemistry / Year: 2001
Title: Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.
Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
#1: Journal: Biochemistry / Year: 2001
Title: Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity.
Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
#2: Journal: J.BIOL.INORG.CHEM. / Year: 1998
Title: Crystal Structure of Escherichia coli Manganese Superoxide Dismutase at 2.1 A Resolution
Authors: Edwards, R.A. / Baker, H.M. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N.
History
DepositionMar 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 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)92,1438
Polymers91,9244
Non-polymers2204
Water5,567309
1
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0724
Polymers45,9622
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area17680 Å2
MethodPISA
2
C: MANGANESE SUPEROXIDE DISMUTASE
D: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0724
Polymers45,9622
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.845, 108.893, 182.882
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-555-

HOH

21C-555-

HOH

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Components

#1: Protein
MANGANESE SUPEROXIDE DISMUTASE


Mass: 22980.879 Da / Num. of mol.: 4 / Mutation: Y34F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PDT1-5 / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 20% w/v PEG 6000, 0.1 M bicine, 25 mM sodium azide, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %(w/v)PEG60001reservoir
20.1 MBicine1reservoirpH8.3
325 mM1reservoirNaN3
49.0 mg/mlprotein1dropin water

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→38.85 Å / Num. all: 43949 / Num. obs: 43949 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.298 / Num. unique all: 1198 / % possible all: 79.2
Reflection
*PLUS
Num. measured all: 348981
Reflection shell
*PLUS
% possible obs: 79.2 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2220 -RANDOM
Rwork0.167 ---
all-43928 --
obs-43928 97.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.882 Å20 Å20 Å2
2---0.303 Å20 Å2
3---4.185 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 8 305 6821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.05279
X-RAY DIFFRACTIONc_angle_deg1.20524
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.1871.5
X-RAY DIFFRACTIONc_mcangle_it1.9792
X-RAY DIFFRACTIONc_scbond_it2.0362
X-RAY DIFFRACTIONc_scangle_it3.0842.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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