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- PDB-1hcx: Choline binding domain of the major autolysin (C-LytA) from Strep... -

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Basic information

Entry
Database: PDB / ID: 1hcx
TitleCholine binding domain of the major autolysin (C-LytA) from Streptococcus pneumoniae
ComponentsMAJOR AUTOLYSIN
KeywordsCHOLINE-BINDING DOMAIN / CELL WALL ATTACHMENT
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Cholin Binding / left handed beta-beta-3-solenoid / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Cholin Binding / left handed beta-beta-3-solenoid / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
CHOLINE ION / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride / Autolysin
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsFernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factor Lyta
Authors: Fernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A.
#1: Journal: Gene / Year: 1990
Title: Cloning and Expression of Gene Fragments Encoding the Choline-Binding Domain of Pneumococcal Murein Hydrolases
Authors: Sanchez-Puelles, J.M. / Sanz, J.M. / Garcia, J.L. / Garcia, E.
History
DepositionMay 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR AUTOLYSIN
B: MAJOR AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,28610
Polymers29,8992
Non-polymers1,3878
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.049, 118.177, 104.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.58348, -0.21209, 0.78395), (-0.05414, -0.95299, -0.29811), (0.81032, -0.21638, 0.54457)
Vector: 20.79011, 70.87526, 1.14969)

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Components

#1: Protein MAJOR AUTOLYSIN / C-LYTA / CELL WALL BINDING DOMAIN


Mass: 14949.556 Da / Num. of mol.: 2 / Fragment: CHOLINE-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / Gene: LYTA / Plasmid: PCE17 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-TPT / 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride


Mass: 463.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClN3Pt
#3: Chemical
ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H14NO
#4: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.4
Details: 30% PEG 4000, 0.2 M NA-ACETATE, 0.1 M AMMONIUM-ACETATE, PH 6.4, 0.15 M CHOLINE-CL, 0.4 MM DDAO.
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 Msodium citrate1reservoirpH6.4
40.4 mMDDOA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9840,1.0695,1.0715
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9841
21.06951
31.07151
ReflectionResolution: 2.6→35 Å / Num. obs: 11378 / % possible obs: 99.7 % / Observed criterion σ(I): 8 / Redundancy: 4.5 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.049 / Net I/σ(I): 18
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.266 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 35 Å / Num. measured all: 105081 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→34.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1255263.49 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1169 10.3 %RANDOM
Rwork0.239 ---
obs0.239 11378 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.4388 Å2 / ksol: 0.318346 e/Å3
Displacement parametersBiso mean: 48.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.22 Å20 Å20 Å2
2---12.1 Å20 Å2
3----2.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 82 79 2283
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 168 8.9 %
Rwork0.345 1717 -
obs--100 %
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 35 Å / % reflection Rfree: 10 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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