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- PDB-8vep: Crystal structure of transpeptidase domain of PBP2 from Neisseria... -

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Basic information

Entry
Database: PDB / ID: 8vep
TitleCrystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by piperacillin
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / penicillin-binding protein / transpeptidase / complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / 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
Piperacillin (Open Form) / DI(HYDROXYETHYL)ETHER / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.002 Å
AuthorsStratton, C.M. / Bala, S. / Davies, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI164794 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Ureidopenicillins Are Potent Inhibitors of Penicillin-Binding Protein 2 from Multidrug-Resistant Neisseria gonorrhoeae H041.
Authors: Turner, J.M. / Stratton, C.M. / Bala, S. / Cardenas Alvarez, M. / Nicholas, R.A. / Davies, C.
History
DepositionDec 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9873
Polymers35,3611
Non-polymers6262
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.621, 61.621, 110.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable peptidoglycan D,D-transpeptidase PenA / Penicillin-binding protein 2 / PBP-2


Mass: 35361.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Piperacillin / Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: H041 / Gene: penA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): K12
References: UniProt: F2Z7K9, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-JPP / Piperacillin (Open Form)


Mass: 519.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.5 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.8 / Details: 32-40% PEG 600, 0.1 M CHES / PH range: 9.3-10.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.07 Å / Num. obs: 23839 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.074 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2303 / CC1/2: 0.829 / Rpim(I) all: 0.246 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000v720data scaling
HKL-2000v720data reduction
REFMAC5.8.0267phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.002→46.07 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.797 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1158 4.858 %RANDOM
Rwork0.17 22679 --
all0.172 ---
obs-23837 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å20 Å2
2---0.992 Å2-0 Å2
3---0.262 Å2
Refinement stepCycle: LAST / Resolution: 2.002→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 43 185 2681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122593
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162466
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6733531
X-RAY DIFFRACTIONr_angle_other_deg0.51.5765739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.466516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27110431
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3791096
X-RAY DIFFRACTIONr_chiral_restr0.0730.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022940
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_nbd_refined0.2090.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22281
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21288
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2163
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0550.25
X-RAY DIFFRACTIONr_nbd_other0.0960.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.216
X-RAY DIFFRACTIONr_mcbond_it1.5811.6731312
X-RAY DIFFRACTIONr_mcbond_other1.5811.6731312
X-RAY DIFFRACTIONr_mcangle_it2.4422.4971643
X-RAY DIFFRACTIONr_mcangle_other2.4412.51644
X-RAY DIFFRACTIONr_scbond_it2.2672.0441281
X-RAY DIFFRACTIONr_scbond_other2.2662.0461282
X-RAY DIFFRACTIONr_scangle_it3.652.9331882
X-RAY DIFFRACTIONr_scangle_other3.6492.9351883
X-RAY DIFFRACTIONr_lrange_it4.96822.9262893
X-RAY DIFFRACTIONr_lrange_other4.93521.9782852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.0540.231660.221637X-RAY DIFFRACTION97.81
2.054-2.110.255910.2031629X-RAY DIFFRACTION100
2.11-2.1710.182760.1841539X-RAY DIFFRACTION100
2.171-2.2380.204840.1771523X-RAY DIFFRACTION100
2.238-2.3110.234820.171492X-RAY DIFFRACTION99.8731
2.311-2.3920.198670.1681437X-RAY DIFFRACTION99.9336
2.392-2.4820.232690.1651398X-RAY DIFFRACTION100
2.482-2.5830.202580.171339X-RAY DIFFRACTION99.6434
2.583-2.6970.193660.1661280X-RAY DIFFRACTION99.7776
2.697-2.8290.199590.1641239X-RAY DIFFRACTION99.5399
2.829-2.9810.185530.1671174X-RAY DIFFRACTION99.4327
2.981-3.1610.226560.1811108X-RAY DIFFRACTION99.2327
3.161-3.3780.194510.1781032X-RAY DIFFRACTION98.6339
3.378-3.6470.184740.176949X-RAY DIFFRACTION97.9885
3.647-3.9930.184470.153890X-RAY DIFFRACTION98.3211
3.993-4.460.204460.144809X-RAY DIFFRACTION97.7143
4.46-5.1420.176440.13735X-RAY DIFFRACTION99.1094
5.142-6.2780.265270.168646X-RAY DIFFRACTION99.4092
6.278-8.7970.216260.148508X-RAY DIFFRACTION100
8.797-46.0670.246160.211315X-RAY DIFFRACTION99.1018

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