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- PDB-9z0x: Crystal structure of Neisseria gonorrhoeae penicillin-binding pro... -

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Basic information

Entry
Database: PDB / ID: 9z0x
TitleCrystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing seven resistance mutations
ComponentsPenicillin-binding protein 2
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / TRANSPEPTIDASE DOMAIN / N. GONORRHOEAE / ANTIBIOTIC RESISTANCE
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
PHOSPHATE ION / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae FA19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsSingh, A. / Bala, S. / Davies, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI164794-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066861 United States
CitationJournal: To Be Published
Title: Interrogating the Delicate Balance between Antibiotic Resistance and Enzymatic Function in Penicillin-Binding Protein 2 Mutations from Ceftriaxone-Resistant Neisseria gonorrhoeae strain H041
Authors: Bivins, M.M. / Tomberg, J. / Bagshaw, M. / Singh, A. / Bala, S. / Davies, C. / Nicholas, R.A.
History
DepositionNov 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8503
Polymers70,7552
Non-polymers951
Water1,928107
1
A: Penicillin-binding protein 2


Theoretical massNumber of molelcules
Total (without water)35,3771
Polymers35,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4722
Polymers35,3771
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.556, 76.839, 87.478
Angle α, β, γ (deg.)90.00, 92.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35377.352 Da / Num. of mol.: 2 / Mutation: A311V, I312M, V316P, T483S, F504L, N512Y, G545S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA19 (bacteria) / Gene: penA, WHOF_00731, WHOF_01799C / Plasmid: PMALC2KV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0AB74EE38, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 40% PEG 600, 0.1 M CHES / PH range: 9-10

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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: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 46263 / % possible obs: 98.9 % / Redundancy: 6.7 % / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Χ2: 1.207 / Net I/av σ(I): 20.8 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.976.50.5353.646520.8750.9660.2270.5830.52499.7
1.97-2.056.80.40246110.9280.9810.1670.4360.67399.4
2.05-2.146.70.29846280.9580.9890.1230.3230.92299.2
2.14-2.256.50.22745880.9690.9920.0950.2471.24298.4
2.25-2.396.60.17945980.9750.9940.0740.1941.72998.8
2.39-2.587.10.15246580.9830.9960.0610.1641.68199.9
2.58-2.846.90.12546350.9840.9960.0510.1350.92799.7
2.84-3.256.50.10346160.990.9970.0430.1121.04798.5
3.25-4.096.90.08446150.9940.9980.0340.0911.69898.2
4.09-506.70.0746620.9940.9980.0290.0761.56897.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→35.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 14.414 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23883 2155 4.7 %RANDOM
Rwork0.19985 ---
obs0.2017 44090 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å2-2.64 Å2
2---3.17 Å20 Å2
3---5.84 Å2
Refinement stepCycle: 1 / Resolution: 1.9→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 5 107 4994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164868
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.8276803
X-RAY DIFFRACTIONr_angle_other_deg0.6181.7511201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2195647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.501540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4910835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025941
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021139
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_it2.0611.0682573
X-RAY DIFFRACTIONr_mcbond_other2.0591.0672573
X-RAY DIFFRACTIONr_mcangle_it2.971.9013213
X-RAY DIFFRACTIONr_mcangle_other2.971.9023214
X-RAY DIFFRACTIONr_scbond_it2.6311.4292440
X-RAY DIFFRACTIONr_scbond_other2.6111.4162437
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0962.4513581
X-RAY DIFFRACTIONr_long_range_B_refined9.40212.845474
X-RAY DIFFRACTIONr_long_range_B_other9.39112.575462
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.943 Å
RfactorNum. reflection% reflection
Rfree0.285 167 -
Rwork0.259 3055 -
obs--92.59 %
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)
10.4179-0.4230.39850.7548-0.2030.66560.1172-0.0275-0.0395-0.389-0.08250.03560.13570.139-0.03480.93040.05970.09420.5709-0.02430.022618.429-9.5255.621
20.0566-0.1997-0.05840.97030.21960.40960.0230.0047-0.0140.08470.00120.1448-0.01470.0447-0.02420.62870.00320.13760.5722-0.00520.17335.5048.67538.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 573
2X-RAY DIFFRACTION2B236 - 574

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