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- PDB-6p54: Crystal structure of transpeptidase domain of PBP2 from Neisseria... -

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Basic information

Entry
Database: PDB / ID: 6p54
TitleCrystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae acylated by ceftriaxone
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE/ANTIBIOTIC / Penicillin-binding protein / transpeptidase domain / Neisseria gonorrhoeae / antibiotic resistance / HYDROLASE-ANTIBIOTIC 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 / plasma membrane => GO:0005886 / proteolysis
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 domain / Penicillin-binding protein, transpeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ceftriaxone / CEFOTAXIME, C3' cleaved, open, bound form / DI(HYDROXYETHYL)ETHER / ceftriaxone, bound form / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.83 Å
AuthorsSingh, A. / Davies, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066861 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Recognition of the beta-lactam carboxylate triggers acylation ofNeisseria gonorrhoeaepenicillin-binding protein 2.
Authors: Singh, A. / Tomberg, J. / Nicholas, R.A. / Davies, C.
History
DepositionMay 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,2836
Polymers70,6532
Non-polymers1,6314
Water3,783210
1
A: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8992
Polymers35,3261
Non-polymers5731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3844
Polymers35,3261
Non-polymers1,0583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.223, 78.485, 87.608
Angle α, β, γ (deg.)90.00, 91.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35326.262 Da / Num. of mol.: 2 / Fragment: UNP residues 237-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (unknown) / Gene: penA / Plasmid: pMAL-C2KV / Production host: Escherichia coli (E. coli) / Strain (production host): GW6011
References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase

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Non-polymers , 5 types, 214 molecules

#2: Chemical ChemComp-NZV / ceftriaxone, bound form


Mass: 572.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N8O8S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form / Cefotaxime


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#4: Chemical ChemComp-9F2 / Ceftriaxone / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N8O7S3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 0.1 M CHES, 40% PEG600

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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: Feb 7, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→35.01 Å / Num. obs: 50936 / % possible obs: 98.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.041 / Net I/σ(I): 29.1
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2 / Num. unique obs: 2469 / CC1/2: 0.801 / Rpim(I) all: 0.335 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.83→35.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.74 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2584 5.1 %RANDOM
Rwork0.172 ---
obs0.174 48332 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å2-0 Å20.8 Å2
2---2.33 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 1.83→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 105 210 5259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195232
X-RAY DIFFRACTIONr_bond_other_d0.0010.024955
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.997108
X-RAY DIFFRACTIONr_angle_other_deg0.807311461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02922.919209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07115856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4061542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021060
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_it1.9973.1612630
X-RAY DIFFRACTIONr_mcbond_other1.9953.1612630
X-RAY DIFFRACTIONr_mcangle_it2.9784.7323286
X-RAY DIFFRACTIONr_mcangle_other2.9784.7313287
X-RAY DIFFRACTIONr_scbond_it2.833.6682602
X-RAY DIFFRACTIONr_scbond_other2.833.6682602
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5795.3423810
X-RAY DIFFRACTIONr_long_range_B_refined5.98638.1935716
X-RAY DIFFRACTIONr_long_range_B_other5.98538.1975717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.827→1.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 180 -
Rwork0.272 3178 -
obs--88.32 %

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