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- PDB-9md0: Crystal structure of the transpeptidase domain of PBP2 from the N... -

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Basic information

Entry
Database: PDB / ID: 9md0
TitleCrystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6752
ComponentsPenicillin-binding protein 2
KeywordsLIGASE / Neisseria gonorrhoeae cephalosporin resistance Penicillin-binding protein 2 Boronate inhibitor
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 / 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 35/02 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.613 Å
AuthorsStratton, C.M. / Bala, S. / Davies, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141239 United States
CitationJournal: Biorxiv / Year: 2024
Title: A new class of penicillin-binding protein inhibitors to address drug-resistant Neisseria gonorrhoeae.
Authors: Uehara, T. / Zulli, A.L. / Miller, B. / Avery, L.M. / Boyd, S.A. / Chatwin, C.L. / Chu, G.H. / Drager, A.S. / Edwards, M. / Emeigh Hart, S.G. / Myers, C.L. / Rongala, G. / Stevenson, A. / ...Authors: Uehara, T. / Zulli, A.L. / Miller, B. / Avery, L.M. / Boyd, S.A. / Chatwin, C.L. / Chu, G.H. / Drager, A.S. / Edwards, M. / Emeigh Hart, S.G. / Myers, C.L. / Rongala, G. / Stevenson, A. / Uehara, K. / Yi, F. / Wang, B. / Liu, Z. / Wang, M. / Zhao, Z. / Zhou, X. / Zhao, H. / Stratton, C.M. / Bala, S. / Davies, C. / Tkavc, R. / Jerse, A.E. / Pevear, D.C. / Burns, C.J. / Daigle, D.M. / Condon, S.M.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8842
Polymers35,3311
Non-polymers5521
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.464, 60.224, 110.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35331.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae 35/02 (bacteria) / Gene: penA / Plasmid: PMALC2KV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8RR30, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-A1BJB / (3R)-3-({(2R)-2-(4-carboxyphenyl)-2-[(4-ethyl-2,3-dioxopiperazine-1-carbonyl)amino]acetyl}amino)-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid


Mass: 552.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C25H25BN4O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 40% PEG 600, 0.1 M CHES, PH 9.3

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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: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→38.7 Å / Num. obs: 10571 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.08 / Rrim(I) all: 0.215 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 975 / CC1/2: 0.831 / CC star: 0.953 / Rpim(I) all: 0.283 / Rrim(I) all: 0.769 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.613→38.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.229 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R Free: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 514 4.863 %RANDOM
Rwork0.1749 10056 --
all0.178 ---
obs-10570 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.113 Å20 Å2-0 Å2
2---0.149 Å20 Å2
3---0.037 Å2
Refinement stepCycle: LAST / Resolution: 2.613→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 40 19 2509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122560
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162404
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6763479
X-RAY DIFFRACTIONr_angle_other_deg0.5181.5745590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5455329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.623515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71310426
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.5551095
X-RAY DIFFRACTIONr_chiral_restr0.0680.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
X-RAY DIFFRACTIONr_nbd_refined0.2170.2480
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22169
X-RAY DIFFRACTIONr_nbtor_refined0.180.21263
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.251
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.22
X-RAY DIFFRACTIONr_nbd_other0.2180.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2080.24
X-RAY DIFFRACTIONr_mcbond_it2.5032.7651304
X-RAY DIFFRACTIONr_mcbond_other2.5042.7651304
X-RAY DIFFRACTIONr_mcangle_it3.9164.1381631
X-RAY DIFFRACTIONr_mcangle_other3.9144.141632
X-RAY DIFFRACTIONr_scbond_it3.1553.1961256
X-RAY DIFFRACTIONr_scbond_other3.1553.1941253
X-RAY DIFFRACTIONr_scangle_it4.8744.6481846
X-RAY DIFFRACTIONr_scangle_other4.8724.6491847
X-RAY DIFFRACTIONr_lrange_it6.33433.1282740
X-RAY DIFFRACTIONr_lrange_other6.33333.1292741
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.613-2.680.294320.2276680.237590.9420.96992.22660.198
2.68-2.7530.276320.2087140.2117460.9560.9731000.176
2.753-2.8330.329330.2136980.2187330.9480.97399.72710.176
2.833-2.9190.246350.2036740.2057090.9680.9751000.172
2.919-3.0150.262450.2056590.2097040.9570.9741000.173
3.015-3.120.244300.1746340.1786640.9630.9781000.151
3.12-3.2370.211240.1746120.1756360.9590.9811000.152
3.237-3.3680.266300.1786080.1826390.9610.9899.84350.158
3.368-3.5160.25340.1865580.1895920.9590.9791000.166
3.516-3.6860.23320.1675420.1715750.9540.98499.82610.153
3.686-3.8840.221420.1585060.1635550.9720.98698.73870.148
3.884-4.1170.187200.1484960.1495210.9840.98799.04030.142
4.117-4.3980.191240.144620.1424960.9740.98897.98390.13
4.398-4.7450.166240.1354260.1364610.9740.98997.61390.134
4.745-5.190.336120.1634080.1674390.9580.98995.6720.159
5.19-5.790.252180.1843700.1883880.9730.981000.17
5.79-6.660.266180.173350.1733530.9510.9831000.163
6.66-8.0970.224150.1572920.163070.9710.9851000.154
8.097-11.2090.129110.1482370.1472490.9960.98599.59840.152
11.209-38.680.17530.2811560.2791620.9580.9698.14810.297

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