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- PDB-6xqz: Crystal structure of the catalytic domain of PBP2 S310A from Neis... -

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Basic information

Entry
Database: PDB / ID: 6xqz
TitleCrystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae at pH 7.5
ComponentsPeptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / PBP2 / beta-lactam / antibiotic target
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
Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsFenton, B.A. / Zhou, P. / 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: 2021
Title: Mutations in PBP2 from ceftriaxone-resistant Neisseria gonorrhoeae alter the dynamics of the beta 3-beta 4 loop to favor a low-affinity drug-binding state.
Authors: Fenton, B.A. / Tomberg, J. / Sciandra, C.A. / Nicholas, R.A. / Davies, C. / Zhou, P.
History
DepositionJul 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,04610
Polymers70,5692
Non-polymers4778
Water4,864270
1
A: Peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6377
Polymers35,2841
Non-polymers3536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4083
Polymers35,2841
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.540, 77.480, 86.710
Angle α, β, γ (deg.)90.000, 91.872, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLNGLN(chain 'A' and (resid 237 through 241 or resid 244...AA237 - 2413 - 7
12GLNGLNLEULEU(chain 'A' and (resid 237 through 241 or resid 244...AA244 - 25110 - 17
13LYSLYSVALVAL(chain 'A' and (resid 237 through 241 or resid 244...AA253 - 25519 - 21
14TYRTYRALAALA(chain 'A' and (resid 237 through 241 or resid 244...AA257 - 26223 - 28
15VALVALPROPRO(chain 'A' and (resid 237 through 241 or resid 244...AA265 - 28231 - 48
16GLYGLYASPASP(chain 'A' and (resid 237 through 241 or resid 244...AA296 - 30449 - 57
17ILEILEALAALA(chain 'A' and (resid 237 through 241 or resid 244...AA306 - 31059 - 63
18LYSLYSTHRTHR(chain 'A' and (resid 237 through 241 or resid 244...AA313 - 34766 - 100
19VALVALASPASP(chain 'A' and (resid 237 through 241 or resid 244...AA349 - 354102 - 107
110GLYGLYTRPTRP(chain 'A' and (resid 237 through 241 or resid 244...AA357 - 410110 - 163
111PROPROARGARG(chain 'A' and (resid 237 through 241 or resid 244...AA412 - 471165 - 224
112LEULEUTHRTHR(chain 'A' and (resid 237 through 241 or resid 244...AA473 - 500226 - 253
113LYSLYSVALVAL(chain 'A' and (resid 237 through 241 or resid 244...AA513 - 533266 - 286
114ILEILEGLYGLY(chain 'A' and (resid 237 through 241 or resid 244...AA535 - 545288 - 298
115VALVALALAALA(chain 'A' and (resid 237 through 241 or resid 244...AA548 - 574301 - 327
21LEULEUGLNGLN(chain 'B' and (resid 237 through 241 or resid 244...BB237 - 2413 - 7
22GLNGLNLEULEU(chain 'B' and (resid 237 through 241 or resid 244...BB244 - 25110 - 17
23LYSLYSVALVAL(chain 'B' and (resid 237 through 241 or resid 244...BB253 - 25519 - 21
24TYRTYRALAALA(chain 'B' and (resid 237 through 241 or resid 244...BB257 - 26223 - 28
25VALVALPROPRO(chain 'B' and (resid 237 through 241 or resid 244...BB265 - 28231 - 48
26GLYGLYASPASP(chain 'B' and (resid 237 through 241 or resid 244...BB296 - 30449 - 57
27ILEILEALAALA(chain 'B' and (resid 237 through 241 or resid 244...BB306 - 31059 - 63
28LYSLYSTHRTHR(chain 'B' and (resid 237 through 241 or resid 244...BB313 - 34766 - 100
29VALVALASPASP(chain 'B' and (resid 237 through 241 or resid 244...BB349 - 354102 - 107
210GLYGLYTRPTRP(chain 'B' and (resid 237 through 241 or resid 244...BB357 - 410110 - 163
211PROPROARGARG(chain 'B' and (resid 237 through 241 or resid 244...BB412 - 471165 - 224
212LEULEUTHRTHR(chain 'B' and (resid 237 through 241 or resid 244...BB473 - 500226 - 253
213LYSLYSVALVAL(chain 'B' and (resid 237 through 241 or resid 244...BB513 - 533266 - 286
214ILEILEGLYGLY(chain 'B' and (resid 237 through 241 or resid 244...BB535 - 545288 - 298
215VALVALALAALA(chain 'B' and (resid 237 through 241 or resid 244...BB548 - 574301 - 327

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Components

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


Mass: 35284.285 Da / Num. of mol.: 2 / Mutation: S310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: penA / Production host: Escherichia coli (E. coli)
References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 400, 50 mM HEPES (pH 7.5) 25 mM Tris (pH 7.5), 50 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→42.52 Å / Num. obs: 35213 / % possible obs: 98 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.82 Å2 / Rrim(I) all: 0.069 / Net I/σ(I): 16.47
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.09 / Num. unique obs: 3454 / Rrim(I) all: 0.394 / % possible all: 96.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER1.17.1_3660phasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P53

6p53


Resolution: 2.04→42.52 Å / SU ML: 0.2143 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.4199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2125 1761 5 %
Rwork0.1639 33448 -
obs0.1663 35209 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.28 Å2
Refinement stepCycle: LAST / Resolution: 2.04→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4815 0 27 270 5112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755036
X-RAY DIFFRACTIONf_angle_d0.94416840
X-RAY DIFFRACTIONf_chiral_restr0.0565771
X-RAY DIFFRACTIONf_plane_restr0.0066892
X-RAY DIFFRACTIONf_dihedral_angle_d22.05471879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10.26381310.19662487X-RAY DIFFRACTION96.78
2.1-2.160.23681360.18522577X-RAY DIFFRACTION97.31
2.16-2.230.27961330.18042531X-RAY DIFFRACTION96.94
2.23-2.310.22271330.17362537X-RAY DIFFRACTION97.69
2.31-2.40.25161350.17372557X-RAY DIFFRACTION97.64
2.4-2.510.2271360.17162585X-RAY DIFFRACTION97.84
2.51-2.640.21761340.16772533X-RAY DIFFRACTION97.91
2.64-2.80.22081350.17642576X-RAY DIFFRACTION98.22
2.8-3.020.23521360.17452585X-RAY DIFFRACTION98.44
3.02-3.330.21531370.17662591X-RAY DIFFRACTION98.7
3.33-3.810.20461370.16012602X-RAY DIFFRACTION98.77
3.81-4.790.18381380.13882621X-RAY DIFFRACTION99.1
4.79-42.520.17521400.15022666X-RAY DIFFRACTION99.01
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)
11.08798587445-0.303617855069-0.08217700529771.0397409136-0.1761234092550.817236437866-0.01388957020710.02501920108270.0770685749563-0.001653648318-0.0295286154341-0.0494034974377-0.03133390657150.0498225577826-6.27005285536E-50.114500850089-0.0123561567992-0.007205909185950.09256604205950.01006426198530.166226620665-15.8050377819-18.6286204679-37.9841056509
20.3090729654620.10807893048-0.3011986433540.641604381053-0.1989916911051.18664489462-0.0978460165619-0.261314449016-0.1025929510860.113714334552-0.0360838078229-0.06652762142570.03579754082380.329065349387-0.1607713155270.2106555427060.0782479814813-0.00333713934120.3554844188010.09072419249370.193079451377-7.58408905666-39.4625617344-5.24031900362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 236 through 574)
2X-RAY DIFFRACTION2(chain 'B' and resid 237 through 574)

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