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- PDB-9z0w: Crystal structure of Neisseria gonorrhoeae penicillin-binding pro... -

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Basic information

Entry
Database: PDB / ID: 9z0w
TitleCrystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing six 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: 2.15 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)70,8783
Polymers70,7832
Non-polymers951
Water1,36976
1
A: Penicillin-binding protein 2


Theoretical massNumber of molelcules
Total (without water)35,3911
Polymers35,3911
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)35,4862
Polymers35,3911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.883, 77.048, 87.778
Angle α, β, γ (deg.)90.00, 91.95, 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: 35391.379 Da / Num. of mol.: 2 / Mutation: A311V, I312M, V316P, F504L, N512Y, G545S
Source method: isolated from a genetically manipulated source
Details: Transpeptidase domain construct / 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.: 76 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
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: 2.15→35.85 Å / Num. obs: 31068 / % possible obs: 94.7 % / Redundancy: 5 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.063 / Rrim(I) all: 0.143 / Χ2: 1.046 / Net I/av σ(I): 19.1 / Net I/σ(I): 5.9
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
2.15-2.1940.5782.115560.4840.8080.3210.6650.45997.6
2.19-2.234.30.53116290.8020.9440.2810.6030.45898.1
2.23-2.273.60.52815420.4840.8070.310.6160.68395.6
2.27-2.324.80.44115820.8850.9690.2210.4950.47897.6
2.32-2.374.80.3916130.8930.9710.1940.4380.50196.8
2.37-2.424.60.35714890.8490.9580.1840.4040.54693.1
2.42-2.485.40.37116170.8980.9730.1760.4120.53897.5
2.48-2.5560.36716120.9420.9850.1620.4020.54399.7
2.55-2.626.20.3516450.9430.9850.1520.3830.56699.8
2.62-2.715.90.31516130.9480.9870.1410.3460.64799.2
2.71-2.816.20.26616230.9550.9890.1170.2920.68399.1
2.81-2.9260.2316060.9630.9910.1030.2530.83298.8
2.92-3.055.70.18916200.9710.9930.0870.2090.89898.2
3.05-3.215.40.15615880.9730.9930.0740.1741.09996.1
3.21-3.414.90.13414880.970.9920.0680.1511.41892
3.41-3.684.20.10813850.9820.9950.0580.1241.95584.3
3.68-4.054.50.08714710.9860.9960.0460.0992.1788.1
4.05-4.634.30.07213500.9910.9980.0390.0832.42282.7
4.63-5.834.40.06114920.9940.9980.0330.072.68889.6
5.83-504.50.05515470.9950.9990.0290.0623.08590.9

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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: 2.15→35.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.769 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24619 1760 5.7 %RANDOM
Rwork0.18701 ---
obs0.19039 29292 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.081 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0 Å20.22 Å2
2--0.02 Å2-0 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.15→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 5 76 4957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124982
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164834
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.8276755
X-RAY DIFFRACTIONr_angle_other_deg0.5781.7511119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3425638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.326539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50310827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021127
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_it2.853.1392561
X-RAY DIFFRACTIONr_mcbond_other2.8473.1392561
X-RAY DIFFRACTIONr_mcangle_it3.985.6293196
X-RAY DIFFRACTIONr_mcangle_other3.985.633197
X-RAY DIFFRACTIONr_scbond_it3.8233.6572421
X-RAY DIFFRACTIONr_scbond_other3.8163.6532418
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9446.5063554
X-RAY DIFFRACTIONr_long_range_B_refined7.60831.395410
X-RAY DIFFRACTIONr_long_range_B_other7.60231.385403
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.202 Å
RfactorNum. reflection% reflection
Rfree0.278 132 -
Rwork0.237 2199 -
obs--96.92 %
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)
10.4639-0.48710.20361.0306-0.30960.67970.10890.0192-0.0328-0.3046-0.09330.01540.05760.1216-0.01560.37940.0240.02810.0954-0.0130.008618.629-9.4325.592
20.1919-0.1369-0.14810.76620.25320.56340.01330.0115-0.00870.05610.01420.101900.0238-0.02750.24410.01020.06060.08410.00840.06245.7238.64238.297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 573
2X-RAY DIFFRACTION2B236 - 574

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