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

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Basic information

Entry
Database: PDB / ID: 6xqv
TitleCrystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae in a pre-acylation complex with ceftriaxone
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / PBP2 / beta-lactam / antibiotic target / ceftriaxone
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / 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 / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / 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
Ceftriaxone / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / pdbx_initial_refinement_model

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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)72,5569
Polymers70,5692
Non-polymers1,9877
Water4,143230
1
A: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0665
Polymers35,2841
Non-polymers7824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4904
Polymers35,2841
Non-polymers1,2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.600, 77.990, 87.690
Angle α, β, γ (deg.)90.000, 91.109, 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

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Components

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


Mass: 35284.285 Da / Num. of mol.: 2
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-9F2 / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H18N8O7S3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 11% PEG 3350, 0.075 M potassium sulfate, 12.5 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: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→43.84 Å / Num. obs: 35913 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 27.58 Å2 / Rrim(I) all: 0.109 / Net I/σ(I): 11.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.33 / Num. unique obs: 3586 / Rrim(I) all: 0.609 / % possible all: 99.6

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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: 2.05→43.84 Å / SU ML: 0.1811 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.6876
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2028 1795 5 %
Rwork0.1683 34117 -
obs0.17 35912 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.39 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 124 230 5322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00455322
X-RAY DIFFRACTIONf_angle_d0.96147253
X-RAY DIFFRACTIONf_chiral_restr0.0503796
X-RAY DIFFRACTIONf_plane_restr0.0051948
X-RAY DIFFRACTIONf_dihedral_angle_d15.55492092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.26051370.22212610X-RAY DIFFRACTION99.38
2.11-2.170.26051380.21322607X-RAY DIFFRACTION99.78
2.17-2.240.22021380.1952624X-RAY DIFFRACTION99.6
2.24-2.320.25451360.19272580X-RAY DIFFRACTION99.45
2.32-2.410.23981370.18192621X-RAY DIFFRACTION99.35
2.41-2.520.23131400.17342653X-RAY DIFFRACTION99.82
2.52-2.650.221370.17442599X-RAY DIFFRACTION99.71
2.65-2.820.23021390.17222637X-RAY DIFFRACTION99.75
2.82-3.040.19991380.17122619X-RAY DIFFRACTION99.67
3.04-3.340.20871380.17162618X-RAY DIFFRACTION99.57
3.34-3.820.19111370.15672629X-RAY DIFFRACTION98.93
3.83-4.820.17381400.14212661X-RAY DIFFRACTION99.93
4.82-43.840.16381400.16092659X-RAY DIFFRACTION98.35
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)
11.357122236590.160194859504-0.03496041744130.644016591137-0.1067996822170.9262709924210.285095279283-0.5170779108170.01264912880240.522016664062-0.4417976201990.290075224810.150447985681-0.1517455640280.5270775048370.197244951849-0.06776168419050.09558050507280.330075631375-0.08220902899870.203088458723-12.515879126524.24425987387.13313070302
20.3796748409480.4533906260820.1711031546550.543037023992-0.2231657931961.080396047350.00767239688836-0.07398809199590.128511948841-0.106091608906-0.03901440080.108200797729-0.2064784758040.0265484507945-0.01837450596810.195575833357-0.02378790897210.002052767465010.127397600452-0.006752276087170.1968847456440.47289473854233.3908075344-13.2176143311
30.377037406844-0.306033415111-0.3442112368110.559462538584-0.02577066984230.902722155276-0.09007380810560.136003831554-0.00156966472704-0.1324224762910.1182618994050.0893842168227-0.0615380750899-0.04698608539286.75383236711E-50.185686929714-0.0186924109203-0.003299279327950.1565039988350.007769392064610.16428927262-4.793088641426.0337214246-15.7212540684
40.108589050080.142615535959-0.03668171353320.0774628234910.01649656318790.0758153259193-0.07388933669020.1940451598510.2881232728870.173373418117-0.311478912264-0.0515106001459-0.007040202628710.0856106559269-0.0001654029452990.3731619133240.0180687560224-0.06221448644660.26275799424-0.01170130858020.346761774658-7.3417959490132.1131492657-25.106773988
51.048728724310.319788866411-0.3460012186950.900626980180.09143256433971.01978876720.0234998827684-0.133973566078-0.05206862853030.0728120776614-0.0716748964111-0.0739664132790.04849290432080.0538225230255-0.0005547084555910.128761054253-0.00721571370565-0.02127630628350.1457671426290.004628196021880.174196521722-0.17349373299319.859417687-4.80686802087
61.741146364890.559071869749-0.6101997532090.7424944820780.8160953711691.113285047130.169117667466-0.09068198401480.1826609683680.00891290113531-0.1689211367090.177262515283-0.141189076729-0.0906764152393-0.02836794731090.165769514115-0.0003806406495260.01294058439390.18742305483-0.05692321755850.200440933307-7.0535598677434.6712415-2.9173793558
70.8157390600680.0403483719995-0.3665742538580.4000722488160.01699237489490.179595136470.0427119697817-0.7221871077440.1372255438980.294855033975-0.0912169843029-0.2582791346310.0149746288790.0279303797636-0.002535562415470.260266978352-0.0945811528988-0.02160089482180.374475743342-0.00177352757930.1869589694790.53089283734825.103879602911.0076425041
80.754640439379-1.02689168410.1502290689741.30129697458-0.14566037110.8562021454490.0347963500540.4735950103880.193692745225-0.1746757259090.01453398747180.147748093662-0.2315035690750.02022515733370.003156466180390.227449050560.0142307889464-0.009959736974850.2699521434950.005654292939730.225975825414-19.097198428613.78917804-50.4993863908
90.6031300113050.11908657366-0.4669065466440.9314817118140.2577095547670.260906162378-0.0644058325505-0.01754924206210.01484107206440.035965761994-0.01257156475470.0393176565070.0537123949802-0.02152243966613.55567572319E-50.221932614774-0.0101634103781-0.007543334917250.172721400615-0.01453814162360.188528186411-13.047464330.650268285525-29.8473416313
100.1820675502970.6566564448230.04152666777041.310739779530.5373861517640.953984283342-0.0509060359074-0.0120974446520.0330504964652-0.04981232363290.005752934313310.1005926567480.000788466125013-0.0765525297983-1.48372249799E-50.242349796062-0.0178236880686-0.01341715693050.221006727227-0.02346194856120.222943911849-12.56966560814.19983761771-28.7335265761
110.678630551066-0.1502946108150.1326716966580.9358718165880.07138501390831.475373908-0.007986611635310.07323063538350.03057407059440.0396094428362-0.02249474389610.00775678515897-0.0236956668610.0377315667345-2.93689519325E-60.158549223128-0.02205096892180.004001457703090.169369563143-0.01074409445820.185730046129-8.519363369198.11388282107-35.7247737189
120.830537096436-0.5968175461480.5155691833761.61335044810.137459918570.161398727662-0.0894629804674-0.170980805343-0.032021169624-0.0284437030522-0.02161226428830.249287157364-0.007803043757-0.0243245209323-0.002727618617530.183495843411-0.007634444654450.001041383280240.245178351267-0.02365298122450.186144955261-17.22251490483.32133021227-45.0569188074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 235 through 294 )
2X-RAY DIFFRACTION2chain 'A' and (resid 295 through 354 )
3X-RAY DIFFRACTION3chain 'A' and (resid 355 through 405 )
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 420 )
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 494 )
6X-RAY DIFFRACTION6chain 'A' and (resid 495 through 544 )
7X-RAY DIFFRACTION7chain 'A' and (resid 545 through 574 )
8X-RAY DIFFRACTION8chain 'B' and (resid 235 through 294 )
9X-RAY DIFFRACTION9chain 'B' and (resid 295 through 344 )
10X-RAY DIFFRACTION10chain 'B' and (resid 345 through 405 )
11X-RAY DIFFRACTION11chain 'B' and (resid 406 through 494 )
12X-RAY DIFFRACTION12chain 'B' and (resid 495 through 574 )

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