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- PDB-6hzj: Apo structure of TP domain from clinical penicillin-resistant mut... -

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Basic information

Entry
Database: PDB / ID: 6hzj
TitleApo structure of TP domain from clinical penicillin-resistant mutant Neisseria gonorrhoea strain 6140 Penicillin-Binding Protein 2 (PBP2)
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / penicillin-binding protein / transpeptidase
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 / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / plasma membrane => GO:0005886 / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable peptidoglycan D,D-transpeptidase PenA / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae FA6140 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsBellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)grant.MR/P007503/1 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance.
Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
History
DepositionOct 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,9932
Polymers72,9932
Non-polymers00
Water7,296405
1
A: Probable peptidoglycan D,D-transpeptidase PenA


Theoretical massNumber of molelcules
Total (without water)36,4971
Polymers36,4971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable peptidoglycan D,D-transpeptidase PenA


Theoretical massNumber of molelcules
Total (without water)36,4971
Polymers36,4971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.645, 77.594, 81.866
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36496.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA6140 (bacteria)
Gene: penA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E5KLA8, UniProt: P08149*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1 M sodium citrate and 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.43→56.01 Å / Num. obs: 115424 / % possible obs: 96.1 % / Redundancy: 4.1 % / Rrim(I) all: 0.189 / Net I/σ(I): 4.6
Reflection shellResolution: 1.43→1.45 Å / Num. unique obs: 5082

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
XSCALEdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u3t

4u3t


Resolution: 1.43→56.01 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.474 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30149 5428 5 %RANDOM
Rwork0.27753 ---
obs0.27874 104114 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.682 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å2-0 Å2-0.13 Å2
2---0.92 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.43→56.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 0 405 5373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195067
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9696867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75223.048210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7215843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4071542
X-RAY DIFFRACTIONr_chiral_restr0.0770.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213836
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.526 262 -
Rwork0.515 5196 -
obs--62.05 %

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