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- PDB-1xtm: Crystal structure of the double mutant Y88H-P104H of a SOD-like p... -

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Basic information

Entry
Database: PDB / ID: 1xtm
TitleCrystal structure of the double mutant Y88H-P104H of a SOD-like protein from Bacillus subtilis.
ComponentsHypothetical superoxide dismutase-like protein yojM
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SOD / Cu-Zn SOD / SOD-like / superoxide dismutase mutants
Function / homology
Function and homology information


ion binding / superoxide dismutase activity / removal of superoxide radicals / copper ion binding / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Prokaryotic lipoprotein-attachment site / Prokaryotic lipoprotein-attachment site / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase-like protein YojM
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCalderone, V. / Mangani, S. / Banci, L. / Benvenuti, M. / Bertini, I. / Fantoni, A. / Viezzoli, M.S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: From an Inactive Prokaryotic SOD Homologue to an Active Protein through Site-Directed Mutagenesis.
Authors: Banci, L. / Benvenuti, M. / Bertini, I. / Cabelli, D.E. / Calderone, V. / Fantoni, A. / Mangani, S. / Migliardi, M. / Viezzoli, M.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.
Authors: Banci, L. / Bertini, I. / Calderone, V. / Cramaro, F. / Del Conte, R. / Fantoni, A. / Mangani, S. / Quattrone, A. / Viezzoli, M.S.
History
DepositionOct 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hypothetical superoxide dismutase-like protein yojM
A: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9649
Polymers37,5102
Non-polymers4547
Water4,071226
1
B: Hypothetical superoxide dismutase-like protein yojM
hetero molecules

A: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9649
Polymers37,5102
Non-polymers4547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_547-x+1/2,y-1/2,-z+21
Buried area1300 Å2
ΔGint-125 kcal/mol
Surface area13760 Å2
MethodPISA
2
A: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8843
Polymers18,7551
Non-polymers1292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0806
Polymers18,7551
Non-polymers3255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.462, 104.350, 58.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe protein is a monomer in vivo but there are two molecules.

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Components

#1: Protein Hypothetical superoxide dismutase-like protein yojM


Mass: 18754.797 Da / Num. of mol.: 2 / Mutation: Y67H, P83H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): TOP1 / References: UniProt: O31851
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na Acetate, 30% PEG4000, 0.2M Ammonium Sulphate, 1mM ZnCl2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.2768 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 2004 / Details: Double crystal focussing mono chromator
RadiationMonochromator: Double crystal focussing mono chromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2768 Å / Relative weight: 1
ReflectionResolution: 1.6→28.8 Å / Num. all: 43173 / Num. obs: 43173 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 21.907 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 9.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6245 / Rsym value: 0.478 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S4I

1s4i


Resolution: 1.6→25.6 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.43 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.121 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26628 3320 7.7 %RANDOM
Rwork0.25279 ---
all0.25381 39853 --
obs0.25381 39853 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.866 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--2.06 Å20 Å2
3----0.7 Å2
Refine analyzeLuzzati sigma a obs: 0.084 Å
Refinement stepCycle: LAST / Resolution: 1.6→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 7 226 2507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9313138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.2085303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98225.439114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56415369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22158
X-RAY DIFFRACTIONr_chiral_restr0.1310.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021822
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21081
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21502
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1831.51544
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66222372
X-RAY DIFFRACTIONr_scbond_it2.3463850
X-RAY DIFFRACTIONr_scangle_it3.5124.5766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free22.78137
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 243 -
Rwork0.416 2927 -
obs--100 %

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