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- PDB-2ip6: Crystal structure of PedB -

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Basic information

Entry
Database: PDB / ID: 2ip6
TitleCrystal structure of PedB
ComponentsPapB
KeywordsANTIMICROBIAL PROTEIN / immunity protein to the pediocin PP-1
Function / homologyde novo design (two linked rop proteins) - #140 / : / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / Immunity protein
Function and homology information
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsKang, S.O. / Kim, I.K. / Kim, M.K. / Kim, J.H. / Yim, H.S. / Cha, S.S.
Citation
Journal: Bmc Struct.Biol. / Year: 2007
Title: High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins
Authors: Kim, I.K. / Kim, M.K. / Kim, J.H. / Yim, H.S. / Cha, S.S. / Kang, S.O.
#1: Journal: Biochim.Biophys.Acta / Year: 2005
Title: Crystallization and preliminary X-ray crystallographic analysis of the pediocin immunity protein (PedB) from Pediococcus pentosaceus at 1.35 A resolution
Authors: Kim, I.K. / Kim, M.K. / Yim, H.S. / Cha, S.S. / Kang, S.O.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1082
Polymers13,0121
Non-polymers961
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.189, 62.189, 39.898
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein PapB / PedB


Mass: 13011.685 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q79IK2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.711271 Å3/Da / Density % sol: 28.123611 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6
Details: 2.4M ammonium sulfate, 0.3M sodium chloride, 0.1M MES, pH 6.0, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97900, 0.97911, 0.97137
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Apr 2, 2005
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979111
30.971371
ReflectionResolution: 1.35→30 Å / Num. all: 19433 / Num. obs: 18937 / % possible obs: 97.4 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073
Reflection shellResolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2.6 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→18.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1071505.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1867 9.9 %RANDOM
Rwork0.209 ---
obs0.209 18937 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8088 Å2 / ksol: 0.358512 e/Å3
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å21.44 Å20 Å2
2--1.95 Å20 Å2
3----3.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.35→18.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 0 5 160 867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 274 9 %
Rwork0.268 2767 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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