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- PDB-2bml: Ofloxacin-like antibiotics inhibit pneumococcal cell wall degradi... -

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Basic information

Entry
Database: PDB / ID: 2bml
TitleOfloxacin-like antibiotics inhibit pneumococcal cell wall degrading virulence factors
ComponentsAUTOLYSIN
KeywordsCHOLINE-BINDING DOMAIN / CELL WALL ATTACHMENT / OFLOXACIN-LIKE ANTIBIOTICS
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
DEXTROFLOXACINE / Autolysin
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFernandez-Tornero, C. / Gimenez-Gallego, G. / Romero, A. / Garcia, E. / Pascual-Teresa, B.D. / Lopez, R.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Ofloxacin-Like Antibiotics Inhibit Pneumococcal Cell Wall-Degrading Virulence Factors
Authors: Fernandez-Tornero, C. / Garcia, E. / Lopez, R. / Pascual-Teresa, B.D. / Gimenez-Gallego, G. / Romero, A.
#1: 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. / Garcia, E. / Lopez, R. / Gimenez-Gallego, G. / Romero, A.
History
DepositionMar 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AUTOLYSIN
B: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,43811
Polymers29,7852
Non-polymers1,6539
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.670, 94.480, 38.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.95447, 0.29818, 0.00892), (0.27834, 0.90092, -0.33299), (-0.10733, -0.31534, -0.94289)
Vector: 59.54821, -3.8016, 30.12691)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AUTOLYSIN / / N-ACETYLMURAMOYL-L-ALANINE AMIDASE / MUREIN / HYDROLASE / MUCOPEPTIDE AMINOHYDROLASE / CELL WALL HYDROLASE


Mass: 14892.502 Da / Num. of mol.: 2 / Fragment: CHOLINE-BINDING DOMAIN, RESIDUES 193-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Plasmid: PCE17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase

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Non-polymers , 6 types, 64 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-XED / DEXTROFLOXACINE


Mass: 361.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20FN3O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.88 Å3/Da / Density % sol: 56.92 %
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN FROM A 12 MG/ML PROTEIN SOLUTION OVER A WELL SOLUTION CONTAINING 2M AMMONIUM SULPHATE AND 2% (W/V) PEG 400 BUFFERED WITH 0.1M HEPES (PH 7.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0163
DetectorType: MARRESEARCH / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0163 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 9193 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.6
Reflection shellResolution: 2.6→20 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.6 / % possible all: 91.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCX

1hcx


Resolution: 2.6→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 704892.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 743 8.1 %RANDOM
Rwork0.22 ---
obs0.22 9145 84.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.541 Å2 / ksol: 0.676592 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.61 Å20 Å20 Å2
2--9.6 Å20 Å2
3----3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 108 55 2271
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_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 2.6→2.75 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 135 8.6 %
Rwork0.326 1436 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4DEXTRO.PARAMDEXTRO.TOP
X-RAY DIFFRACTION5PEGTRIS.PARAMPEGTRIS.TOP

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