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- PDB-6xv5: Crystal structure of penicillin-binding protein 2 from Yersinia p... -

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Basic information

Entry
Database: PDB / ID: 6xv5
TitleCrystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with ertapenem
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsMEMBRANE PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein / peptidoglycan crosslinking / ertapenem
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
L(+)-TARTARIC ACID / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.673 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
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
BBB: Peptidoglycan D,D-transpeptidase MrdA
AAA: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1753
Polymers132,0252
Non-polymers1501
Water2,684149
1
BBB: Peptidoglycan D,D-transpeptidase MrdA


Theoretical massNumber of molelcules
Total (without water)66,0121
Polymers66,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1622
Polymers66,0121
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.265, 147.772, 164.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains BBB AAA)

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Components

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


Mass: 66012.406 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, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: Crystals were grown in a condition containing 1 uL of 1 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM ertapenem) and 2 uL of reservoir solution (0.5 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.67→109.937 Å / Num. obs: 38541 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.2
Reflection shellResolution: 2.701→7.331 Å / Rmerge(I) obs: 0.04 / Num. unique obs: 2108 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
STARANISOdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TII

6tii


Resolution: 2.673→109.937 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.883 / SU B: 18.456 / SU ML: 0.351 / Cross valid method: FREE R-VALUE / ESU R Free: 0.461
RfactorNum. reflection% reflection
Rfree0.2851 1485 4.834 %
Rwork0.213 --
all0.216 --
obs-30718 77.249 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.278 Å20 Å20 Å2
2--0.125 Å20 Å2
3----0.402 Å2
Refinement stepCycle: LAST / Resolution: 2.673→109.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8499 0 10 149 8658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138758
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178142
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.65611898
X-RAY DIFFRACTIONr_angle_other_deg1.1021.57818881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.79251072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94721.5460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.737151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9481565
X-RAY DIFFRACTIONr_chiral_restr0.0530.21140
X-RAY DIFFRACTIONr_chiral_restr_other0.1180.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029797
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021866
X-RAY DIFFRACTIONr_nbd_refined0.1950.21802
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.27914
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24107
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.216
X-RAY DIFFRACTIONr_nbd_other0.2440.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0690.23
X-RAY DIFFRACTIONr_mcbond_it3.1948.2184288
X-RAY DIFFRACTIONr_mcbond_other3.1918.2174286
X-RAY DIFFRACTIONr_mcangle_it5.38112.3145357
X-RAY DIFFRACTIONr_mcangle_other5.3812.3145357
X-RAY DIFFRACTIONr_scbond_it2.6588.5944470
X-RAY DIFFRACTIONr_scbond_other2.6598.5924467
X-RAY DIFFRACTIONr_scangle_it4.70712.7456540
X-RAY DIFFRACTIONr_scangle_other4.70712.7446539
X-RAY DIFFRACTIONr_lrange_it8.55194.139693
X-RAY DIFFRACTIONr_lrange_other8.5194.1279679
X-RAY DIFFRACTIONr_ncsr_local_group_10.1120.0516451
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
2.673-2.7420.486150.4131540.4228510.6690.6975.92770.42
2.742-2.8170.269250.3626000.35828660.6350.69721.80740.356
2.817-2.8990.4470.339460.33327030.7330.77236.7370.326
2.899-2.9880.339690.29315090.29526850.7880.82358.7710.28
2.988-3.0860.353960.28518260.28825820.7920.81274.43840.27
3.086-3.1940.3311060.29419590.29624910.7990.80982.89840.276
3.194-3.3140.323990.28621620.28824760.8350.82891.31660.266
3.314-3.450.3291160.2721800.27322960.850.8571000.241
3.45-3.6030.3111090.25421380.25722470.8430.8881000.228
3.603-3.7780.307890.22720750.2321640.8820.911000.204
3.778-3.9830.2661140.20619460.20920600.9080.9321000.189
3.983-4.2240.2331060.19418390.19619450.9320.941000.176
4.224-4.5150.246750.17717570.1818320.9210.9451000.163
4.515-4.8760.289980.17516140.18117120.9050.9461000.166
4.876-5.340.28690.18515170.18915860.9390.9471000.174
5.34-5.9690.303800.19113680.19614480.9060.9471000.182
5.969-6.8890.304430.18312610.18713040.9230.9491000.18
6.889-8.4290.252500.17710480.1810980.9230.9541000.185
8.429-11.8850.203480.1538330.1568820.9560.97399.88660.171
11.885-109.9370.374310.3055010.3085370.8770.90399.06890.341

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