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- PDB-7ajx: The X-ray Structure of L,D-transpeptidase LdtA from Vibrio choler... -

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Basic information

Entry
Database: PDB / ID: 7ajx
TitleThe X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem
ComponentsL,D-transpeptidase YcbB
KeywordsTRANSFERASE / L / D-transpeptidase
Function / homology
Function and homology information


peptidoglycan biosynthetic process / carboxypeptidase activity / transferase activity
Similarity search - Function
L,D-transpeptidase, scaffold domain / Scaffold domain / PGBD superfamily / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily
Similarity search - Domain/homology
Chem-MXR / L,D-transpeptidase YcbB
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBatuecas, M.T. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-90030-P Spain
CitationJournal: To Be Published
Title: The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem
Authors: Batuecas, M.T. / Hermoso, J.A.
History
DepositionSep 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L,D-transpeptidase YcbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8663
Polymers60,4181
Non-polymers4482
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint4 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.877, 101.224, 115.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L,D-transpeptidase YcbB


Mass: 60418.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013138_01558, ERS013186_00077, ERS013206_00149 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A655UKB5
#2: Chemical ChemComp-MXR / (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / meropenem bound form (tautomerism)


Mass: 385.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C17H27N3O5S / Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013138_01558, ERS013186_00077, ERS013206_00149 / Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1M HEPES pH 7 + 10% PEG 8000 + 10% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.55→46.386 Å / Num. obs: 22790 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rpim(I) all: 0.068 / Net I/σ(I): 9.2
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2750 / CC1/2: 0.516 / Rpim(I) all: 1.038 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AJ9

7aj9


Resolution: 2.55→46.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.229 / SU ML: 0.316 / Cross valid method: FREE R-VALUE / ESU R: 0.473 / ESU R Free: 0.3
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.267 1104 4.856 %
Rwork0.209 21633 -
all0.212 --
obs-22737 99.838 %
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: 64.039 Å2
Baniso -1Baniso -2Baniso -3
1--5.689 Å20 Å2-0 Å2
2--0.087 Å20 Å2
3---5.602 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 4 75 4071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134099
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173820
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.6575590
X-RAY DIFFRACTIONr_angle_other_deg1.1881.5838783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66123.013229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96815640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0521524
X-RAY DIFFRACTIONr_chiral_restr0.0680.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024655
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02959
X-RAY DIFFRACTIONr_nbd_refined0.2160.2778
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.23449
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21943
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.216
X-RAY DIFFRACTIONr_nbd_other0.2260.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.29
X-RAY DIFFRACTIONr_mcbond_it4.146.4921959
X-RAY DIFFRACTIONr_mcbond_other4.1396.4891957
X-RAY DIFFRACTIONr_mcangle_it6.3359.7372447
X-RAY DIFFRACTIONr_mcangle_other6.3359.7372447
X-RAY DIFFRACTIONr_scbond_it4.7047.0622140
X-RAY DIFFRACTIONr_scbond_other4.7037.0622141
X-RAY DIFFRACTIONr_scangle_it7.47610.3953143
X-RAY DIFFRACTIONr_scangle_other7.47510.3953144
X-RAY DIFFRACTIONr_lrange_it9.49174.7624390
X-RAY DIFFRACTIONr_lrange_other9.4974.7564390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.41730.3781578X-RAY DIFFRACTION99.9395
2.616-2.6880.353840.3511537X-RAY DIFFRACTION99.8153
2.688-2.7660.364960.3321461X-RAY DIFFRACTION99.9358
2.766-2.8510.305790.3281443X-RAY DIFFRACTION100
2.851-2.9440.378880.2911381X-RAY DIFFRACTION99.5257
2.944-3.0470.365660.271381X-RAY DIFFRACTION100
3.047-3.1620.278710.2451304X-RAY DIFFRACTION99.8548
3.162-3.2910.281570.2181283X-RAY DIFFRACTION100
3.291-3.4370.266690.2051215X-RAY DIFFRACTION100
3.437-3.6040.29540.1831188X-RAY DIFFRACTION100
3.604-3.7990.254550.1811105X-RAY DIFFRACTION99.9139
3.799-4.0290.222510.1651064X-RAY DIFFRACTION100
4.029-4.3060.257470.1771001X-RAY DIFFRACTION100
4.306-4.650.234450.156944X-RAY DIFFRACTION100
4.65-5.0910.233400.174859X-RAY DIFFRACTION99.778
5.091-5.6890.224420.193796X-RAY DIFFRACTION100
5.689-6.5630.314310.217703X-RAY DIFFRACTION99.8639
6.563-8.0230.298220.189618X-RAY DIFFRACTION99.844
8.023-11.2840.128210.149486X-RAY DIFFRACTION99.2172
11.284-46.340.267130.223286X-RAY DIFFRACTION95.5272

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