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

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Basic information

Entry
Database: PDB / ID: 7ajo
TitleThe X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with the cross-linking reaction intermediate
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-S2K / L,D-transpeptidase YcbB
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 the cross-linking reaction intermediate
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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)60,7993
Polymers60,4181
Non-polymers3812
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint4 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.849, 102.328, 113.226
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-S2K / (2~{S},6~{S})-2-azanyl-6-[[(4~{R})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]heptanedioic acid


Mass: 319.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M 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: 1.85→46.67 Å / Num. obs: 58138 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rpim(I) all: 0.069 / Net I/σ(I): 9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 6.4 / Num. unique obs: 3549 / CC1/2: 0.409 / Rpim(I) all: 1.042 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AJ9

7aj9


Resolution: 1.85→46.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.995 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 2982 5.1 %RANDOM
Rwork0.1811 ---
obs0.1831 55081 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.67 Å2 / Biso mean: 30.197 Å2 / Biso min: 15.11 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å2-0 Å20 Å2
2--0.43 Å2-0 Å2
3---2.06 Å2
Refinement stepCycle: final / Resolution: 1.85→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3999 0 8 467 4474
Biso mean--23.53 42.17 -
Num. residues----492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134133
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173852
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.6485636
X-RAY DIFFRACTIONr_angle_other_deg1.3911.588859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5455499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47723.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04415646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0911524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02974
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 251 -
Rwork0.354 4026 -
all-4277 -
obs--99.88 %

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