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- PDB-6tii: Crystal structure of penicillin-binding protein 2 from Yersinia pestis -

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Basic information

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


peptidoglycan L,D-transpeptidase activity / 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
BROMIDE ION / Peptidoglycan D,D-transpeptidase MrdA / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPankov, G. / Hunter, W.N. / Dawson, A.
CitationJournal: To Be Published
Title: The structure of penicillin-binding protein 2 from Yersinia pestis
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)131,2664
Polymers131,1062
Non-polymers1602
Water5,495305
1
AAA: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6332
Polymers65,5531
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6332
Polymers65,5531
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.661, 84.773, 88.359
Angle α, β, γ (deg.)113.467, 94.972, 103.725
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: Branched rectangular prisms
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 1 uL of 1 mg/ml YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 2 uL reservoir solution (containing 0.1 M HEPES-NaOH pH 7.5, 0.5 M K+/Na+ tartrate and 10 mM NaBr)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→79.36 Å / Num. obs: 56420 / % possible obs: 90.2 % / Redundancy: 5.5 % / CC1/2: 0.781 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.095 / Rrim(I) all: 0.163 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4462 / CC1/2: 0.703 / Rpim(I) all: 0.632 / Rrim(I) all: 0.756 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LP4

5lp4


Resolution: 2.26→50.005 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.2 / SU ML: 0.255 / Cross valid method: FREE R-VALUE / ESU R: 0.353 / ESU R Free: 0.252
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2525 2616 5.012 %
Rwork0.1914 --
all0.194 --
obs-52196 90.395 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.592 Å2
Baniso -1Baniso -2Baniso -3
1--2.724 Å2-4.025 Å2-3.875 Å2
2--0.136 Å21.946 Å2
3---2.622 Å2
Refinement stepCycle: LAST / Resolution: 2.26→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8420 0 2 305 8727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138642
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178091
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.6511729
X-RAY DIFFRACTIONr_angle_other_deg1.2221.57718767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.41151069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25621.648449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.271151469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9051564
X-RAY DIFFRACTIONr_chiral_restr0.0670.21124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021829
X-RAY DIFFRACTIONr_nbd_refined0.1920.21771
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.27914
X-RAY DIFFRACTIONr_nbtor_refined0.1630.24137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2359
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.230
X-RAY DIFFRACTIONr_nbd_other0.2480.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2960.24
X-RAY DIFFRACTIONr_mcbond_it4.2725.1334285
X-RAY DIFFRACTIONr_mcbond_other4.2675.1314283
X-RAY DIFFRACTIONr_mcangle_it6.3897.6815351
X-RAY DIFFRACTIONr_mcangle_other6.3897.6815351
X-RAY DIFFRACTIONr_scbond_it4.5585.6774357
X-RAY DIFFRACTIONr_scbond_other4.5575.6784358
X-RAY DIFFRACTIONr_scangle_it7.0028.2816378
X-RAY DIFFRACTIONr_scangle_other7.0028.2816379
X-RAY DIFFRACTIONr_lrange_it9.72859.439654
X-RAY DIFFRACTIONr_lrange_other9.71459.3649607
X-RAY DIFFRACTIONr_ncsr_local_group_10.1010.0516728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.26-2.3190.3821870.3834630.3843190.4080.38784.51030.355
2.319-2.3820.3262070.336280.30141180.6580.64293.12770.29
2.382-2.4510.3331730.27935800.28140530.6750.72592.59810.267
2.451-2.5260.2881750.25134160.25339080.8050.80391.88840.239
2.526-2.6090.2841860.22532960.22838120.8230.84191.34310.214
2.609-2.70.3061740.23231300.23636990.8530.84489.32140.213
2.7-2.8020.3141430.21527970.2235180.840.87883.57020.204
2.802-2.9160.2661810.19529850.19934230.8760.992.4920.185
2.916-3.0450.2911640.20329180.20733070.8340.89193.19630.196
3.045-3.1930.2731490.20227360.20530920.8690.89193.30530.196
3.193-3.3650.2861260.23826080.2429850.5480.63991.59130.234
3.365-3.5680.2811070.2323790.23228280.5350.74287.90660.229
3.568-3.8130.2551060.16421650.16826550.9150.94185.53670.163
3.813-4.1160.2061160.14221970.14624480.9460.95194.48530.144
4.116-4.5060.2021030.12620340.1322850.950.96593.5230.133
4.506-5.0330.2051020.12917490.13420430.950.96790.60210.137
5.033-5.8020.244750.16514620.16918200.9220.95384.45050.173
5.802-7.0820.181700.14914120.15115460.9480.95395.86030.157
7.082-9.9160.19480.13310300.13611870.9480.95990.81720.146
9.916-50.0050.189240.1915860.1916770.9470.95890.10340.224

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