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

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Basic information

Entry
Database: PDB / ID: 2wad
TitlePENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)
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
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / : / Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain / Ubiquitin Ligase Nedd4; Chain: W; / 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 / Other non-globular ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / : / Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain / Ubiquitin Ligase Nedd4; Chain: W; / 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 / Other non-globular / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Special / 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 / Penicillin-binding protein 2B
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)222,03512
Polymers221,4473
Non-polymers5899
Water10,269570
1
A: PENICILLIN-BINDING PROTEIN 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0124
Polymers73,8161
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PENICILLIN-BINDING PROTEIN 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0124
Polymers73,8161
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PENICILLIN-BINDING PROTEIN 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0124
Polymers73,8161
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)128.788, 128.788, 123.139
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A86 - 185
2115B86 - 185
3115C86 - 185
1215A196 - 213
2215B196 - 213
3215C196 - 213
1314A50 - 85
2314B50 - 85
3314C50 - 85
1414A186 - 195
2414B186 - 195
3414C186 - 195
1514A214 - 310
2514B214 - 310
3514C214 - 310
1614A548 - 566
2614B548 - 566
3614C548 - 566
1711A311 - 547
2711B311 - 547
3711C311 - 547
1811A567 - 680
2811B567 - 680
3811C567 - 680
1916A700 - 702
2916B700 - 702
3916C700 - 702

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 2B


Mass: 73815.508 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: 5204
References: UniProt: P0A3M6, UniProt: B0B6I9*PLUS, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPBP2B STRAIN R6 P0A3M6 PROTEIN SEQUENCE CODE IS THE CLOSER ONE TO MUTANT STRAIN 5204 (58 MUTATIONS). ...PBP2B STRAIN R6 P0A3M6 PROTEIN SEQUENCE CODE IS THE CLOSER ONE TO MUTANT STRAIN 5204 (58 MUTATIONS). THE PROTEIN SEQUENCE OF PBP2B STRAIN 5204 WAS OBTAINED BY OUR COLLABORATOR (REFERENCE 1 PAGLIERO ET AL. 2004, WITH OUT BEEN SUBMITED TO THE DATABASES). HOWEVER THE PBP2B 5204 TRANSPEPTIDASE DOMAIN ALONE AS BEEN SEQUENCE AND SUBMITED TO THE DATABASE (Q5ZGA5). LAST MODIFIED JULY 22, 2008. VERSION 14.

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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: 2.3 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 8
Details: 100 MM BIS-TRIS-HCL PH 5.5, 300 MM NACL, 5 MM ZN ACETATE, 30% W/V POLYETHYLENE GLYCOL MME 550

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID14-310.931
SYNCHROTRONESRF BM30A21.282740, 1.283334, 1.279625
Detector
TypeIDDetectorDate
ADSC CCD1CCDJun 10, 2007
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9311
21.282741
31.2833341
41.2796251
ReflectionResolution: 2.18→44.5 Å / Num. obs: 108466 / % possible obs: 91 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Biso Wilson estimate: 46.42 Å2 / Rsym value: 0.07 / Net I/σ(I): 17.34
Reflection shellResolution: 2.18→2.31 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.97 / Rsym value: 0.6 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.18→44.5 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.858 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 5889 5 %RANDOM
Rwork0.211 ---
obs0.213 110872 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.18→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13812 0 9 570 14391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.96419144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18451813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7426.087598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.945152345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8391530
X-RAY DIFFRACTIONr_chiral_restr0.1090.22210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110607
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_it1.5421.59027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.533214575
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.09935056
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9924.54569
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2526tight positional0.240.05
2B2526tight positional0.250.05
3C2526tight positional0.250.05
1A1637medium positional1.580.5
2B1637medium positional1.980.5
3C1637medium positional1.350.5
1A404loose positional2.845
2B404loose positional3.145
3C404loose positional2.25
1A2526tight thermal3.840.5
2B2526tight thermal2.990.5
3C2526tight thermal4.80.5
1A1637medium thermal6.482
2B1637medium thermal8.672
3C1637medium thermal5.982
1A404loose thermal4.4410
2B404loose thermal9.1910
3C404loose thermal7.1210
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 399
Rwork0.341 6874
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.15250.05410.01260.09080.02470.18820.01530.0140.070.0306-0.01170.0414-0.0361-0.0282-0.00360.02130.00170.01630.00850.00450.03720.7909-38.45061.8705
20.06010.05630.04210.3420.01850.31850.019-0.0184-0.02830.0755-0.00210.1364-0.0081-0.0177-0.01690.0187-0.00210.02260.00830.01690.105921.6863-37.9928-0.0718
30.3052-0.21930.01710.1701-0.02590.1324-0.00310.0362-0.13040.0010.00490.09390.042-0.0254-0.00180.029-0.01390.00460.0583-0.01530.055821.3965-38.2422-6.2874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 185
2X-RAY DIFFRACTION1B86 - 185
3X-RAY DIFFRACTION1C86 - 185
4X-RAY DIFFRACTION1A196 - 213
5X-RAY DIFFRACTION1B196 - 213
6X-RAY DIFFRACTION1C196 - 213
7X-RAY DIFFRACTION2A50 - 85
8X-RAY DIFFRACTION2B52 - 85
9X-RAY DIFFRACTION2C50 - 85
10X-RAY DIFFRACTION2A186 - 195
11X-RAY DIFFRACTION2B186 - 195
12X-RAY DIFFRACTION2C186 - 195
13X-RAY DIFFRACTION2A214 - 310
14X-RAY DIFFRACTION2B214 - 310
15X-RAY DIFFRACTION2C214 - 310
16X-RAY DIFFRACTION2A548 - 566
17X-RAY DIFFRACTION2B548 - 566
18X-RAY DIFFRACTION2C548 - 566
19X-RAY DIFFRACTION3A311 - 547
20X-RAY DIFFRACTION3B311 - 547
21X-RAY DIFFRACTION3C311 - 547
22X-RAY DIFFRACTION3A567 - 680
23X-RAY DIFFRACTION3B567 - 680
24X-RAY DIFFRACTION3C567 - 680

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