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- PDB-5lp4: Penicillin-Binding Protein (PBP2) from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5lp4
TitlePenicillin-Binding Protein (PBP2) from Helicobacter pylori
ComponentsPenicillin-binding protein 2 (Pbp2)
KeywordsHYDROLASE/ANTIBIOTIC / TRANSFERASE / CELL WALL / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / plasma membrane
Similarity search - Function
Penicillin-binding protein 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/transpeptidase-like
Similarity search - Domain/homology
Penicillin-binding protein 2 (Pbp2)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsContreras-Martel, C. / Martins, A. / Ecobichon, C. / Maragno, D.M. / Mattei, P.J. / El Ghachi, M. / Boneca, I.G. / Dessen, A.
Funding support France, Brazil, 3items
OrganizationGrant numberCountry
French National Research Agency13-BSV8-0015-01 France
FAPESP11/52067-6 Brazil
ERC202283 France
CitationJournal: Nat Commun / Year: 2017
Title: Molecular architecture of the PBP2-MreC core bacterial cell wall synthesis complex.
Authors: Contreras-Martel, C. / Martins, A. / Ecobichon, C. / Trindade, D.M. / Mattei, P.J. / Hicham, S. / Hardouin, P. / Ghachi, M.E. / Boneca, I.G. / Dessen, A.
History
DepositionAug 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 2 (Pbp2)
B: Penicillin-binding protein 2 (Pbp2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7225
Polymers135,4342
Non-polymers2883
Water43224
1
A: Penicillin-binding protein 2 (Pbp2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8132
Polymers67,7171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein 2 (Pbp2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9093
Polymers67,7171
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.397, 140.965, 81.297
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A45 - 588
2010B45 - 588

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Components

#1: Protein Penicillin-binding protein 2 (Pbp2)


Mass: 67716.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_1565 / Plasmid: pACYDuet / Cell line (production host): Novagen / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O26085
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.17 Å3/Da / Density % sol: 43.26 % / Description: Tiny needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.4M (NH4)2SO4, 50MM HEPES-NA PH 7

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979526 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979526 Å / Relative weight: 1
ReflectionResolution: 3.03→45.39 Å / Num. obs: 27837 / % possible obs: 90.8 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 37.46 Å2 / Rsym value: 0.12 / Net I/σ(I): 12.15
Reflection shellResolution: 3.03→3.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.01 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBN

3pbn


Resolution: 3.03→45.39 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.831 / SU ML: 0.47 / Cross valid method: THROUGHOUT / ESU R Free: 0.538 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28766 2766 9.9 %RANDOM
Rwork0.25097 ---
obs0.25467 25070 91.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.474 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å2-0.46 Å2
2---4.12 Å2-0 Å2
3---1.83 Å2
Refinement stepCycle: 1 / Resolution: 3.03→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8332 0 15 24 8371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198526
X-RAY DIFFRACTIONr_bond_other_d0.0030.028338
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.97311534
X-RAY DIFFRACTIONr_angle_other_deg0.819319208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49251043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63725.144383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.326151537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5811529
X-RAY DIFFRACTIONr_chiral_restr0.070.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219584
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021929
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_it2.0813.6874184
X-RAY DIFFRACTIONr_mcbond_other2.0813.6874183
X-RAY DIFFRACTIONr_mcangle_it3.625.5265223
X-RAY DIFFRACTIONr_mcangle_other3.625.5265224
X-RAY DIFFRACTIONr_scbond_it1.8473.9134342
X-RAY DIFFRACTIONr_scbond_other1.843.9054331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2775.7596294
X-RAY DIFFRACTIONr_long_range_B_refined5.9929.1859873
X-RAY DIFFRACTIONr_long_range_B_other5.9929.1869874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 66942 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.032→3.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 173 -
Rwork0.37 1556 -
obs--76.57 %
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)
10.5774-0.46680.31741.3915-0.82920.8362-0.0758-0.04650.02950.12330.09010.0552-0.109-0.085-0.01440.04310.0175-0.00740.1839-0.01650.0115-38.326-72.392317.534
20.5844-0.58420.43251.4312-0.64150.8637-0.0006-0.059-0.0674-0.01390.05490.17370.0645-0.0683-0.05430.0178-0.0340.00010.2076-0.02020.0298-24.7686-134.925335.2084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 700
2X-RAY DIFFRACTION2B45 - 701

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