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- PDB-4ozk: Crystal structure of Laterosporulin, a broad spectrum leaderless ... -

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Basic information

Entry
Database: PDB / ID: 4ozk
TitleCrystal structure of Laterosporulin, a broad spectrum leaderless bacteriocin produced by Brevibacillus laterosporus strain GI-9
ComponentsPutative bacteriocin
KeywordsTOXIN / Bacteriocin / Class IId / leaderless / Defensin-like / antimicrobial / heat stable
Function / homologyLaterosporulin defensin-like peptide / Laterosporulin defensin-like peptide / Putative bacteriocin
Function and homology information
Biological speciesBrevibacillus laterosporus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / SIRAS / molecular replacement / Resolution: 2.038 Å
AuthorsVipul, S. / Thakur, K.G.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific and Insdustrial Research, Govt. of India India
CitationJournal: Febs J. / Year: 2015
Title: The intramolecular disulfide-stapled structure of laterosporulin, a class IId bacteriocin, conceals a human defensin-like structural module.
Authors: Singh, P.K. / Solanki, V. / Sharma, S. / Thakur, K.G. / Krishnan, B. / Korpole, S.
History
DepositionFeb 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_nat / pdbx_database_status ...entity_src_nat / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative bacteriocin


Theoretical massNumber of molelcules
Total (without water)5,6251
Polymers5,6251
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.000, 65.000, 65.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21A-114-

HOH

31A-119-

HOH

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Components

#1: Protein/peptide Putative bacteriocin


Mass: 5625.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brevibacillus laterosporus (bacteria) / Strain: GI-9 / References: UniProt: H1ZZ98
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.5, 3M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.038→65 Å / Num. all: 3319 / Num. obs: 3319 / % possible obs: 98.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 21.9 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.122 / Rsym value: 0.11 / Net I/av σ(I): 6.533 / Net I/σ(I): 17 / Num. measured all: 34934
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.03-2.1410.30.4361.844994380.1460.4365.392.8
2.14-2.2710.80.389248274460.130.3896.2100
2.27-2.4310.80.3222.444924150.1050.3227.4100
2.43-2.62110.2752.843323950.0890.2758.8100
2.62-2.8810.60.1844.138913670.0610.18412.9100
2.88-3.2110.80.0918.436753400.030.09122.1100
3.21-3.7110.70.05812.931662970.0190.05831.9100
3.71-4.5510.40.04514.427832680.0150.04539.3100
4.55-6.439.80.05111.920932140.0180.05136.1100
6.43-45.9628.50.03716.911761390.0150.0373598.7

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Phasing

Phasing
Method
SIRAS
molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.96 Å
Translation2.5 Å45.96 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
SHELXDphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.038→29.069 Å / FOM work R set: 0.8177 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 144 4.36 %
Rwork0.1962 3155 -
obs0.1976 3299 99.67 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.079 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso max: 68.24 Å2 / Biso mean: 24.09 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.038→29.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms388 0 0 23 411
Biso mean---22.5 -
Num. residues----49
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007402
X-RAY DIFFRACTIONf_angle_d1.049541
X-RAY DIFFRACTIONf_chiral_restr0.0754
X-RAY DIFFRACTIONf_plane_restr0.00469
X-RAY DIFFRACTIONf_dihedral_angle_d13.143137
LS refinement shellResolution: 2.0382→2.1111 Å / Total num. of bins used: 1 /
Num. reflection% reflection
Rfree18 -
Rwork290 -
obs-97.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.62093.74040.07727.3626-0.0472.759-0.14760.83580.2989-0.9653-0.23990.8260.4551-0.42910.14580.1425-0.0115-0.04230.1916-0.05310.1296-15.3601-13.3601-24.1566
24.06930.98464.54280.23861.09895.0684-0.4158-0.17590.3111-0.2944-0.04290.1844-0.1592-0.09370.12730.2017-0.01220.00860.1283-0.06490.0742-8.7096-16.915-15.6526
34.85652.94170.34565.52590.02640.20890.27140.0251-0.36720.4136-0.083-0.8294-0.00290.0724-0.11930.17460.0086-0.04220.07720.00220.16082.4912-7.4303-14.4758
46.98434.62183.81556.43164.23275.7470.0373-0.04540.15620.3225-0.27360.14390.3791-0.02960.15970.1820.0488-0.01540.073-0.00810.1071-4.0727-10.0292-16.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:8)A2 - 8
2X-RAY DIFFRACTION2chain 'A' and (resseq 9:14)A9 - 14
3X-RAY DIFFRACTION3chain 'A' and (resseq 15:34)A15 - 34
4X-RAY DIFFRACTION4chain 'A' and (resseq 35:50)A35 - 50

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