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- PDB-6vbm: Crystal structure of a S310A mutant of PBP2 from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 6vbm
TitleCrystal structure of a S310A mutant of PBP2 from Neisseria gonorrhoeae
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / TRANSPEPTIDASE DOMAIN / ANTIBIOTIC RESISTANCE
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.71 Å
AuthorsSingh, A. / 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: 2020
Title: Mutations in Neisseria gonorrhoeae penicillin-binding protein 2 associated with extended-spectrum cephalosporin resistance create an energetic barrier against acylation via restriction of protein dynamics
Authors: Singh, A. / Turner, J. / Tomberg, J. / Fedarovich, A. / Unemo, M. / Nicholas, R.A. / Davies, C.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)70,8104
Polymers70,6212
Non-polymers1902
Water3,297183
1
A: Probable peptidoglycan D,D-transpeptidase PenA


Theoretical massNumber of molelcules
Total (without water)35,3101
Polymers35,3101
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)35,5003
Polymers35,3101
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.594, 77.007, 87.889
Angle α, β, γ (deg.)90.00, 92.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35310.262 Da / Num. of mol.: 2 / Mutation: S310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: penA / Plasmid: pMALC2KV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 0.1 M CHES, 40% PEG 600

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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: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→39.1 Å / Num. obs: 63070 / % possible obs: 98.6 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.034 / Net I/σ(I): 45.9
Reflection shellResolution: 1.71→1.75 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / Num. unique obs: 2904 / CC1/2: 0.904 / Rpim(I) all: 0.206 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6P53

6p53


Resolution: 1.71→39.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.139 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 3128 5 %RANDOM
Rwork0.19368 ---
obs0.19509 59920 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.074 Å2
Baniso -1Baniso -2Baniso -3
1-4.24 Å20 Å21.29 Å2
2---1.95 Å20 Å2
3----2.39 Å2
Refinement stepCycle: 1 / Resolution: 1.71→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 10 183 5051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194984
X-RAY DIFFRACTIONr_bond_other_d0.0010.024749
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9696762
X-RAY DIFFRACTIONr_angle_other_deg0.758310987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89723.069202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48915822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2661539
X-RAY DIFFRACTIONr_chiral_restr0.0750.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021009
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_it1.7993.4282563
X-RAY DIFFRACTIONr_mcbond_other1.793.4272562
X-RAY DIFFRACTIONr_mcangle_it2.6825.133200
X-RAY DIFFRACTIONr_mcangle_other2.6855.1313201
X-RAY DIFFRACTIONr_scbond_it2.383.8392421
X-RAY DIFFRACTIONr_scbond_other2.3733.8322413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.855.6143547
X-RAY DIFFRACTIONr_long_range_B_refined5.02841.0625434
X-RAY DIFFRACTIONr_long_range_B_other5.01540.9665407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.753 Å
RfactorNum. reflection% reflection
Rfree0.335 200 -
Rwork0.289 3786 -
obs--84.61 %

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