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- PDB-2waf: PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMON... -

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Basic information

Entry
Database: PDB / ID: 2waf
TitlePENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN R6)
ComponentsPENICILLIN-BINDING PROTEIN 2B
KeywordsPEPTIDE BINDING PROTEIN / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / TRANSMEMBRANE / ANTIBIOTIC RESISTANCE / CELL SHAPE / PEPTIDOGLYCAN / CELL MEMBRANE / CELL WALL BIOGENESIS/DEGRADATION / MEMBRANE / INFECTION / RESISTANCE / ANTIBIOTIC
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane => GO:0005886
Similarity search - Function
Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein 2B
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsContreras-Martel, C. / Dahout-Gonzalez, C. / Dos-Santos-Martins, A. / Kotnik, M. / Dessen, A.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Pbp Active Site Flexibility as the Key Mechanism for Beta-Lactam Resistance in Pneumococci
Authors: Contreras-Martel, C. / Dahout-Gonzalez, C. / Dos-Santos-Martins, A. / Kotnik, M. / Dessen, A.
#1: Journal: Antimicrob.Agents Chemother. / Year: 2004
Title: Biochemical Characterization of Streptococcus Pneumoniae Penicillin-Binding Protein 2B and its Implication in Beta-Lactam Resistance
Authors: Pagliero, E. / Chesnel, L. / Hopkins, J. / Croize, J. / Dideberg, O. / Vernet, T. / Di-Guilmi, A.
History
DepositionFeb 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENICILLIN-BINDING PROTEIN 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2823
Polymers74,2111
Non-polymers712
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)193.897, 51.593, 121.440
Angle α, β, γ (deg.)90.00, 112.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 2B


Mass: 74210.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOCOCCUS PNEUMONIAE (unknown) / Strain: R6
References: UniProt: P0A3M6, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.8 Å3/Da / Density % sol: 67.65 % / Description: NONE
Crystal growpH: 8 / Details: 1.4M (NH4)2SO4, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9312
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9312 Å / Relative weight: 1
ReflectionResolution: 3.29→47.25 Å / Num. obs: 14291 / % possible obs: 82.5 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 69.16 Å2 / Rsym value: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 3.29→3.49 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.82 / Rsym value: 0.44 / % possible all: 54.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WAD
Resolution: 3.29→47.25 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.867 / SU B: 78.151 / SU ML: 0.532 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.538 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 770 4.9 %RANDOM
Rwork0.237 ---
obs0.24 15012 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å22.57 Å2
2---0.08 Å20 Å2
3---4.71 Å2
Refinement stepCycle: LAST / Resolution: 3.29→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4701 0 2 11 4714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9586501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3445617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54126.039207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.99315794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5031511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.53065
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78124941
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5731720
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6364.51560
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.29→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 30 -
Rwork0.356 747 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.77583.71650.26799.8147-1.95745.787-0.1840.64860.0543-0.4826-0.1728-0.6567-0.26660.13210.35680.00230.01490.19250.5369-0.143-0.21218.4994-5.6885-43.4724
210.12761.3193-3.88730.40070.03842.7893-0.44120.2978-0.8039-0.18140.1239-0.05980.46060.28480.3172-0.0009-0.00760.02940.049-0.0860.0771-0.0363-15.0495-19.7435
36.0374-0.9879-0.60262.6441.11965.2117-0.2301-0.1120.510.07430.2196-0.2126-0.5154-0.020.0105-0.5965-0.0487-0.0618-0.62280.1172-0.3896-32.33110.83734.2958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 185
2X-RAY DIFFRACTION1A196 - 213
3X-RAY DIFFRACTION2A52 - 85
4X-RAY DIFFRACTION2A186 - 195
5X-RAY DIFFRACTION2A214 - 310
6X-RAY DIFFRACTION2A548 - 566
7X-RAY DIFFRACTION3A311 - 547
8X-RAY DIFFRACTION3A567 - 682

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