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- PDB-6tix: Crystal structure of penicillin-binding protein 2 from Yersinia p... -

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Basic information

Entry
Database: PDB / ID: 6tix
TitleCrystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsMEMBRANE PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein / peptidoglycan crosslinking / mecillinam
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein 2 / 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
Chem-DH4 / Peptidoglycan D,D-transpeptidase MrdA / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPankov, G. / Hunter, W.N. / Dawson, A.
CitationJournal: To Be Published
Title: The structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam
Authors: Pankov, G.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
AAA: Peptidoglycan D,D-transpeptidase MrdA
BBB: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7614
Polymers131,1062
Non-polymers6552
Water1,874104
1
AAA: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8802
Polymers65,5531
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8802
Polymers65,5531
Non-polymers3271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.172, 84.035, 87.099
Angle α, β, γ (deg.)112.917, 95.306, 104.566
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2


Mass: 65552.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: mrdA, YPO2604 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A384KFW3, UniProt: A0A5P8YJF3*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-DH4 / 2-[(1R)-1-{[(E)-azepan-1-ylmethylidene]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Mecillinam, bound form / Mecillinam


Mass: 327.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H25N3O3S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.6 % / Description: Branched rectangular prisms
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M ...Details: Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000). The size of these crystals was optimised by three rounds of macroseeding into condition containing (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000 and 2 mM mecillinam)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.8→45.693 Å / Num. obs: 27215 / % possible obs: 92.9 % / Redundancy: 2.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.097 / Net I/σ(I): 4.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4118 / CC1/2: 0.677 / Rpim(I) all: 0.452 / Rrim(I) all: 0.64 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LP4

5lp4


Resolution: 2.8→45.693 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.214 / SU B: 29.964 / SU ML: 0.529 / Average fsc free: 0.7294 / Average fsc work: 0.772 / Cross valid method: FREE R-VALUE / ESU R Free: 0.48
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2902 1308 4.831 %
Rwork0.228 25768 -
all0.231 --
obs-27076 92.432 %
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: 66.303 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å2-8.426 Å2-6.118 Å2
2--1.424 Å24.642 Å2
3---3.222 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 0 104 8270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138355
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177816
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.65411341
X-RAY DIFFRACTIONr_angle_other_deg1.0911.57818119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7851020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13621.59434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.661151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0941560
X-RAY DIFFRACTIONr_chiral_restr0.0460.21091
X-RAY DIFFRACTIONr_chiral_restr_other0.0350.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021757
X-RAY DIFFRACTIONr_nbd_refined0.1950.22136
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.28798
X-RAY DIFFRACTIONr_nbtor_refined0.1620.24009
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23930
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.239
X-RAY DIFFRACTIONr_nbd_other0.2370.2150
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2470.28
X-RAY DIFFRACTIONr_mcbond_it3.2026.9834113
X-RAY DIFFRACTIONr_mcbond_other3.2026.9834112
X-RAY DIFFRACTIONr_mcangle_it5.3310.4635122
X-RAY DIFFRACTIONr_mcangle_other5.32910.4645123
X-RAY DIFFRACTIONr_scbond_it2.7117.3394242
X-RAY DIFFRACTIONr_scbond_other2.7117.3394243
X-RAY DIFFRACTIONr_scangle_it4.72810.8696219
X-RAY DIFFRACTIONr_scangle_other4.72710.8696220
X-RAY DIFFRACTIONr_lrange_it8.63282.4379706
X-RAY DIFFRACTIONr_lrange_other8.63182.4429705
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0516393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.872-2.9510.38950.341878X-RAY DIFFRACTION95.3601
2.951-3.0360.3711080.3181884X-RAY DIFFRACTION96.3716
3.036-3.1290.397990.2961774X-RAY DIFFRACTION95.7077
3.129-3.2310.422880.2811789X-RAY DIFFRACTION95.4245
3.231-3.3440.306770.2631693X-RAY DIFFRACTION96.8801
3.344-3.4690.308840.2571656X-RAY DIFFRACTION95.4995
3.469-3.610.271640.2281546X-RAY DIFFRACTION94.6502
3.61-3.770.287730.2241521X-RAY DIFFRACTION94.3195
3.77-3.9520.298810.2071414X-RAY DIFFRACTION93.3208
3.952-4.1640.269530.1841286X-RAY DIFFRACTION89.7453
4.164-4.4150.274680.1711214X-RAY DIFFRACTION88.7812
4.415-4.7160.198570.1721062X-RAY DIFFRACTION84.1353
4.716-5.090.261540.1871009X-RAY DIFFRACTION84.4321
5.09-5.5680.355510.214964X-RAY DIFFRACTION87.8028
5.568-6.2140.279420.191903X-RAY DIFFRACTION90
6.214-7.1540.197360.179804X-RAY DIFFRACTION91.5033
7.154-8.7080.257300.2661X-RAY DIFFRACTION88.7035

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