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- PDB-3lyy: Crystal structure of the MucBP domain of the adhesion protein PEP... -

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Basic information

Entry
Database: PDB / ID: 3lyy
TitleCrystal structure of the MucBP domain of the adhesion protein PEPE_0118 from Pediococcus pentosaceus. Northeast Structural Genomics Consortium target id PtR41A
ComponentsAdhesion exoprotein
KeywordsCELL ADHESION / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Cell wall / Peptidoglycan-anchor
Function / homology
Function and homology information


Immunoglobulin-like - #4300 / Mub B2-like domain / Muc B2-like domain / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPediococcus pentosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSeetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the MucBP domain of the adhesion protein PEPE_0118 from Pediococcus pentosaceus. Northeast Structural Genomics Consortium target id PtR41A
Authors: Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesion exoprotein
B: Adhesion exoprotein


Theoretical massNumber of molelcules
Total (without water)23,0882
Polymers23,0882
Non-polymers00
Water5,477304
1
A: Adhesion exoprotein

B: Adhesion exoprotein


Theoretical massNumber of molelcules
Total (without water)23,0882
Polymers23,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_654-x+1,-y,z-11
Buried area1050 Å2
ΔGint-6 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.634, 90.634, 56.991
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 Adhesion exoprotein


Mass: 11544.041 Da / Num. of mol.: 2 / Fragment: sequence database residues 796-902
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus (bacteria) / Strain: ATCC 25745 / 183-1w / Gene: PEPE_0118 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03HU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5M (NH4)2SO4, 20% PEG3000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 52646 / Num. obs: 52646 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 4.8 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.053 / Net I/σ(I): 18.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 15 / Num. unique all: 2701 / Rsym value: 0.34 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 93956.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3954 9.8 %RANDOM
Rwork0.194 ---
obs0.194 40192 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5872 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å20 Å2
2--3.48 Å20 Å2
3----6.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 304 1839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.76
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 649 10 %
Rwork0.214 5819 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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