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- PDB-1s4i: Crystal structure of a SOD-like protein from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1s4i
TitleCrystal structure of a SOD-like protein from Bacillus subtilis
Componentssuperoxide dismutase-like protein yojM
KeywordsOXIDOREDUCTASE / SOD / Cu-Zn SOD / SOD-like / superoxide dismutase
Function / homology
Function and homology information


ion binding / superoxide dismutase activity / removal of superoxide radicals / periplasmic space / copper ion binding / extracellular space / 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 / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase-like protein YojM
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBanci, L. / Bertini, I. / Calderone, V. / Cramaro, F. / Del Conte, R. / Fantoni, A. / Mangani, S. / Quattrone, A. / Viezzoli, M.S.
CitationJournal: 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
DepositionJan 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 300BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THE BIOLOGICAL UNIT APPEARS TO BE A MONOMER.
Remark 999SEQUENCE THE AUTHORS STATE THE SEQUENCE IN THE SEQRES CORRESPONDS TO THE ONE CLONED BUT THEY STATE ...SEQUENCE THE AUTHORS STATE THE SEQUENCE IN THE SEQRES CORRESPONDS TO THE ONE CLONED BUT THEY STATE IT IS LIKELY THAT SOME RESIDUES AT THE N-TERMINUS ARE CLEAVED OFF DURING CRYSTALLISATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,48914
Polymers74,9554
Non-polymers53410
Water7,026390
1
B: superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9054
Polymers18,7391
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9054
Polymers18,7391
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8403
Polymers18,7391
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8403
Polymers18,7391
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
B: superoxide dismutase-like protein yojM
D: superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7457
Polymers37,4782
Non-polymers2675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-145 kcal/mol
Surface area13830 Å2
MethodPISA
6
A: superoxide dismutase-like protein yojM
C: superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7457
Polymers37,4782
Non-polymers2675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-143 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.225, 61.108, 64.915
Angle α, β, γ (deg.)84.35, 76.02, 90.42
Int Tables number1
Space group name H-MP1
DetailsThe protein is a monomer in vivo but there are four molecules in the asymmetric unit.

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Components

#1: Protein
superoxide dismutase-like protein yojM


Mass: 18738.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YOJM, BSU19400 / Production host: Escherichia coli (E. coli) / References: UniProt: O31851, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRIS, Ammonium sulphate, PEG4000, LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.281 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2003
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.281 Å / Relative weight: 1
ReflectionResolution: 1.8→37.07 Å / Num. all: 49677 / Num. obs: 49677 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 29.17 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3958 / Rsym value: 0.23 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→37.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.27 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.179 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 4150 8.4 %RANDOM
Rwork0.22091 ---
all0.22399 45524 --
obs0.22399 45524 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-1.25 Å22.52 Å2
2---1.98 Å2-1.48 Å2
3---1.15 Å2
Refine analyzeLuzzati sigma a obs: 0.125 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 0 10 390 4920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0214620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7751.9516245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.0765601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.220.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023624
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2860.22333
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.219
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.5751.52976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.58424725
X-RAY DIFFRACTIONr_scbond_it3.77131644
X-RAY DIFFRACTIONr_scangle_it5.5714.51520
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free14.179210
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 300
Rwork0.324 3227

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