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- PDB-6vbc: Crystal structure of transpeptidase domain of PBP2 from Neisseria... -

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Basic information

Entry
Database: PDB / ID: 6vbc
TitleCrystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / ANTIBIOTIC RESISTANCE / TRANSPEPTIDASE DOMAIN
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 / plasma membrane => GO:0005886 / proteolysis
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable peptidoglycan D,D-transpeptidase PenA


Theoretical massNumber of molelcules
Total (without water)35,3611
Polymers35,3611
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.429, 61.329, 108.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35361.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (unknown) / Gene: penA / Plasmid: pMAlC2KV / Production host: Escherichia coli BL21(DE3) (unknown)
References: UniProt: F2Z7K9, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 40% PEG 600, 0.1 M CHES

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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: Jul 1, 2019
RadiationMonochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→31.69 Å / Num. obs: 48525 / % possible obs: 98.3 % / Redundancy: 6.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.047 / Net I/σ(I): 31.8
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2372 / CC1/2: 0.851 / Rpim(I) all: 0.268

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→31.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.247 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20028 2347 4.8 %RANDOM
Rwork0.17817 ---
obs0.17921 46125 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0 Å2
2--0.11 Å20 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.55→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 0 153 2606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192564
X-RAY DIFFRACTIONr_bond_other_d0.0010.022484
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9693496
X-RAY DIFFRACTIONr_angle_other_deg0.74735763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14223.50597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98715438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
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_it0.9261.5961315
X-RAY DIFFRACTIONr_mcbond_other0.9241.5941314
X-RAY DIFFRACTIONr_mcangle_it1.5742.391647
X-RAY DIFFRACTIONr_mcangle_other1.5742.3921648
X-RAY DIFFRACTIONr_scbond_it1.3561.8571249
X-RAY DIFFRACTIONr_scbond_other1.3551.8591250
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2172.7091840
X-RAY DIFFRACTIONr_long_range_B_refined3.6219.7042893
X-RAY DIFFRACTIONr_long_range_B_other3.53119.4632863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.552→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 153 -
Rwork0.22 3006 -
obs--87.19 %

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