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- PDB-3o60: The Crystal Structure of Lin0861 from Listeria innocua to 2.8A -

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Basic information

Entry
Database: PDB / ID: 3o60
TitleThe Crystal Structure of Lin0861 from Listeria innocua to 2.8A
ComponentsLin0861 protein
KeywordsStructural Genomics / Unknown function / PSI / MCSG / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homologyTetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha / Lin0861 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsStein, A.J. / Rakowski, E. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of Lin0861 from Listeria innocua to 2.8A
Authors: Stein, A.J. / Rakowski, E. / Feldmann, B. / Joachimiak, A.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin0861 protein
B: Lin0861 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8386
Polymers44,4542
Non-polymers3844
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-57 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.457, 95.457, 96.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Lin0861 protein


Mass: 22227.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92DF2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 297 K / pH: 6
Details: 1.26M Ammonium sulfate, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2010
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.499
ReflectionResolution: 2.8→50 Å / Num. obs: 531 / % possible obs: 2.5 % / Redundancy: 1.1 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.3
Reflection shellResolution: 2.8→50 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.127 / % possible all: 2.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.004data extraction
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.8→42.69 Å / Phase error: 27.03 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.246 1092 5.35 %
Rwork0.22 --
obs0.217 21502 94.9 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.21 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 60.91 Å2
Baniso -1Baniso -2Baniso -3
1-10.125 Å20 Å2-0 Å2
2--10.125 Å20 Å2
3----20.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 20 0 2917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012973
X-RAY DIFFRACTIONf_angle_d1.2194042
X-RAY DIFFRACTIONf_dihedral_angle_d21.2031050
X-RAY DIFFRACTIONf_chiral_restr0.072484
X-RAY DIFFRACTIONf_plane_restr0.005512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8005-2.9480.32861410.32812464X-RAY DIFFRACTION81
2.948-3.13230.30491540.29012653X-RAY DIFFRACTION86
3.1323-3.37370.25731470.25172777X-RAY DIFFRACTION91
3.3737-3.71230.25031610.23122800X-RAY DIFFRACTION92
3.7123-4.24740.24521570.21372882X-RAY DIFFRACTION94
4.2474-5.34320.21481530.18062900X-RAY DIFFRACTION94
5.3432-25.6170.2211470.18822855X-RAY DIFFRACTION92

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