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- PDB-1jmm: Crystal structure of the V-region of Streptococcus mutans antigen I/II -

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Basic information

Entry
Database: PDB / ID: 1jmm
TitleCrystal structure of the V-region of Streptococcus mutans antigen I/II
Componentsprotein I/II V-region
KeywordsIMMUNE SYSTEM / MEMBRANE PROTEIN / Antigen I/II / V-region
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Major cell-surface adhesin PAc / Major cell-surface adhesin PAc / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif ...Major cell-surface adhesin PAc / Major cell-surface adhesin PAc / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Major cell-surface adhesin PAc
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsTroffer-Charlier, N. / Ogier, J. / Moras, D. / Cavarelli, J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of the V-region of Streptococcus mutans Antigen I/II at 2.4 a Resolution Suggests a Sugar Preformed Binding Site
Authors: Troffer-Charlier, N. / Ogier, J. / Moras, D. / Cavarelli, J.
History
DepositionJul 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein I/II V-region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6382
Polymers41,6151
Non-polymers231
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.570, 124.570, 147.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322

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Components

#1: Protein protein I/II V-region / Antigen I/II / PAC PROTEIN / surface antigen pac


Mass: 41615.121 Da / Num. of mol.: 1 / Fragment: V-region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P11657
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 4000, sodium acetate, 0.1M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 or 10 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
21 mMTCEP1drop
315 %(w/v)PEG40001reservoir
40.1 Msodium acetate1reservoirpH4.6
50.1 Mammonium sulfate1reservoir
620 %(v/v)glycerol1reservoir
71 mMTCEP1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.97881,0.97903,0.93928
SYNCHROTRONESRF BM1420.97895
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978811
20.979031
30.939281
40.978951
ReflectionResolution: 2.4→20 Å / Num. all: 49439 / Num. obs: 49439 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 34.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 15.7 / % possible all: 99.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2953108.63 / 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
Rfree0.234 3692 7.5 %RANDOM
Rwork0.207 ---
all0.207 49787 --
obs0.207 49439 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.4426 Å2 / ksol: 0.340433 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.11 Å20.83 Å20 Å2
2---7.11 Å20 Å2
3---14.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 1 262 3171
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it3.022
X-RAY DIFFRACTIONc_scangle_it4.032.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 643 7.7 %
Rwork0.239 7685 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAM
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 7.4 % / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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