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

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Basic information

Entry
Database: PDB / ID: 6xqy
TitleCrystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae at pH 9.5
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / PBP2 / beta-lactam / antibiotic target / TRANSFERASE
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: 1.9 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: Probable peptidoglycan D,D-transpeptidase PenA
B: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6043
Polymers70,5692
Non-polymers351
Water2,558142
1
A: Probable peptidoglycan D,D-transpeptidase PenA


Theoretical massNumber of molelcules
Total (without water)35,2841
Polymers35,2841
Non-polymers00
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)35,3202
Polymers35,2841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.940, 76.550, 87.900
Angle α, β, γ (deg.)90.000, 91.636, 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
11METMETGLNGLN(chain 'A' and (resid 236 through 241 or resid 243...AA236 - 2412 - 7
12ILEILEPROPRO(chain 'A' and (resid 236 through 241 or resid 243...AA243 - 2829 - 48
13GLYGLYALAALA(chain 'A' and (resid 236 through 241 or resid 243...AA296 - 31049 - 63
14LYSLYSVALVAL(chain 'A' and (resid 236 through 241 or resid 243...AA313 - 34466 - 97
15ASPASPVALVAL(chain 'A' and (resid 236 through 241 or resid 243...AA346 - 35599 - 108
16GLYGLYARGARG(chain 'A' and (resid 236 through 241 or resid 243...AA357 - 408110 - 161
17TRPTRPARGARG(chain 'A' and (resid 236 through 241 or resid 243...AA410 - 471163 - 224
18LEULEUVALVAL(chain 'A' and (resid 236 through 241 or resid 243...AA473 - 489226 - 242
19GLYGLYLYSLYS(chain 'A' and (resid 236 through 241 or resid 243...AA491 - 503244 - 256
110LYSLYSPROPRO(chain 'A' and (resid 236 through 241 or resid 243...AA513 - 527266 - 280
111VALVALTYRTYR(chain 'A' and (resid 236 through 241 or resid 243...AA529 - 543282 - 296
112GLYGLYILEILE(chain 'A' and (resid 236 through 241 or resid 243...AA545 - 566298 - 319
113PROPROTHRTHR(chain 'A' and (resid 236 through 241 or resid 243...AA568 - 573321 - 326
21METMETGLNGLN(chain 'B' and (resid 236 through 241 or resid 243...BB236 - 2412 - 7
22ILEILEPROPRO(chain 'B' and (resid 236 through 241 or resid 243...BB243 - 2829 - 48
23GLYGLYALAALA(chain 'B' and (resid 236 through 241 or resid 243...BB296 - 31049 - 63
24LYSLYSVALVAL(chain 'B' and (resid 236 through 241 or resid 243...BB313 - 34466 - 97
25ASPASPVALVAL(chain 'B' and (resid 236 through 241 or resid 243...BB346 - 35599 - 108
26GLYGLYARGARG(chain 'B' and (resid 236 through 241 or resid 243...BB357 - 408110 - 161
27TRPTRPARGARG(chain 'B' and (resid 236 through 241 or resid 243...BB410 - 471163 - 224
28LEULEUVALVAL(chain 'B' and (resid 236 through 241 or resid 243...BB473 - 489226 - 242
29GLYGLYLYSLYS(chain 'B' and (resid 236 through 241 or resid 243...BB491 - 503244 - 256
210LYSLYSPROPRO(chain 'B' and (resid 236 through 241 or resid 243...BB513 - 527266 - 280
211VALVALTYRTYR(chain 'B' and (resid 236 through 241 or resid 243...BB529 - 543282 - 296
212GLYGLYILEILE(chain 'B' and (resid 236 through 241 or resid 243...BB545 - 566298 - 319
213PROPROTHRTHR(chain 'B' and (resid 236 through 241 or resid 243...BB568 - 573321 - 326

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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-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 13% PEG 400, 50 mM KCl, 12.5 mM Tris, 12.5 mM Bis-Tris, 25 mM sodium acetate (pH 9.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→44.92 Å / Num. obs: 46696 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.32 Å2 / Rrim(I) all: 0.052 / Net I/σ(I): 17.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4690 / Rrim(I) all: 0.661 / % possible all: 99.5

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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: 1.9→44.92 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.4315
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1953 2333 5 %
Rwork0.1645 44337 -
obs0.1661 46670 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 1 142 5015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675061
X-RAY DIFFRACTIONf_angle_d0.90226874
X-RAY DIFFRACTIONf_chiral_restr0.0564769
X-RAY DIFFRACTIONf_plane_restr0.0062902
X-RAY DIFFRACTIONf_dihedral_angle_d23.70861893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.28281380.22992618X-RAY DIFFRACTION99.57
1.94-1.980.2841360.21772583X-RAY DIFFRACTION99.41
1.98-2.030.2811350.20852600X-RAY DIFFRACTION99.42
2.03-2.080.25791350.21442568X-RAY DIFFRACTION98.22
2.08-2.130.24381330.19972518X-RAY DIFFRACTION96.12
2.13-2.20.23031360.19432581X-RAY DIFFRACTION99.74
2.2-2.270.2231380.17552628X-RAY DIFFRACTION99.75
2.27-2.350.22321380.1812622X-RAY DIFFRACTION99.82
2.35-2.440.26891370.17612598X-RAY DIFFRACTION99.82
2.44-2.550.20971380.16952621X-RAY DIFFRACTION99.78
2.55-2.690.20551380.17322618X-RAY DIFFRACTION99.49
2.69-2.860.24081380.16992616X-RAY DIFFRACTION99.53
2.86-3.080.18511350.18172573X-RAY DIFFRACTION98.47
3.08-3.390.19741400.17362644X-RAY DIFFRACTION99.89
3.39-3.880.18331380.15372631X-RAY DIFFRACTION99.86
3.88-4.880.16021390.13542635X-RAY DIFFRACTION99.53
4.88-44.920.16171410.14992683X-RAY DIFFRACTION99.12
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)
11.37198051313-0.794423575643-0.2275488975541.835632924010.1243791610371.823572128330.04136302101620.141923895161-0.0671925938601-0.341473697233-0.0658944571826-0.02514609425030.0652672182803-0.01742694027070.0001287643006150.345564457642-0.0302215058808-0.006611288428070.26333057777-0.01954935949270.27453765989418.0244645963-9.4217330238.14175384891
21.70458679368-0.619186008106-0.06418844635020.8389494121150.3873026720120.4255263637090.3535274334280.374553885369-0.317851352075-0.871064888543-0.415396583152-0.161736619770.1742419477380.0526207784474-0.04761416846750.6364053715630.05056956460080.01281582041830.357135055648-0.04022257812970.34287224734419.7676149352-11.953786606-3.97829619095
30.6344927749840.6546189194910.230026594110.890546261795-0.1898988601371.35568839480.116843498531-0.488897953746-0.1969148025310.512177563166-0.02400244554130.2439169553590.253072102083-0.2414170653690.0002702726516470.433068940457-0.04331284327630.1031626507020.4293892845490.01866576342890.3693072283260.6895110669970.033365461768150.701141945
40.610659329461-0.368787968028-0.04643603099751.44702763616-0.1219936450421.50756271347-0.0232904563602-0.03151195267560.0666429570567-0.1189084738930.01378832583780.150340674013-0.0680510193484-0.214565056349-1.31267014713E-50.2181758415270.018930793972-0.005205259388780.307095629873-0.01534273739630.3047556559137.0446581526112.883554952330.0309137524
50.967201357176-0.0168003408367-0.5081236831941.747240572570.4387306446851.74772583552-0.030158536513-0.1197168621160.06909033222940.1068332695690.0275939063626-0.03231675489930.0008237003024440.0512843460512-3.0301652663E-50.1653202708440.00731166758241-0.01760696990970.280385085057-0.02663154862920.27705517573711.08939443637.2971737884835.9195047688
60.03283724962430.0234062277181-0.1028385437740.232651862561-0.03795956292440.351282781604-0.107018271713-0.0704372013078-0.1078245503980.2248789707050.04119917230650.172962002579-0.137319982411-0.163774154636-0.0540238502510.2033305249920.01256186840940.04706596098420.402028481258-0.04870772910890.402331451009-5.419406557568.9476854456936.2123847415
70.3122302675760.181372215983-0.1002019795370.5767986157320.4975231695250.642146888748-0.013493950186-0.06382415323120.9424009991110.463580649397-0.02570713076390.0758367413509-0.149816608271-0.125361498865-0.007189598896460.3366520702040.03988541290160.06290117505110.3913966227250.02484931213390.5175165177941.872922630710.428883026646.1977253655
80.06345906906220.1811832411410.1358317197630.3940113429280.3305331376080.2622209029910.0557304963923-0.1578580684220.1333894359880.448131625650.0238308459231-0.0103573579613-0.158461705888-0.06316284336720.0001509653210490.494362940807-0.01811354150020.0002396752943890.435403136515-0.05278444387330.3459886207289.2469368966110.09794045755.5323437834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 236 through 494 )
2X-RAY DIFFRACTION2chain 'A' and (resid 495 through 573 )
3X-RAY DIFFRACTION3chain 'B' and (resid 236 through 281 )
4X-RAY DIFFRACTION4chain 'B' and (resid 282 through 405 )
5X-RAY DIFFRACTION5chain 'B' and (resid 406 through 494 )
6X-RAY DIFFRACTION6chain 'B' and (resid 495 through 522 )
7X-RAY DIFFRACTION7chain 'B' and (resid 523 through 544 )
8X-RAY DIFFRACTION8chain 'B' and (resid 545 through 574 )

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