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

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Basic information

Entry
Database: PDB / ID: 7ajz
TitleThe X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with NAG-NAM(tetrapeptide)
Components
  • L,D-transpeptidase YcbB
  • NAG-NAM(tetrapeptide)
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-AMV / polypeptide(D) / L,D-transpeptidase YcbB
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 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 NAG-NAM(tetrapeptide)
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 2.0Dec 21, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_name_com.entity_id / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 3.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L,D-transpeptidase YcbB
B: L,D-transpeptidase YcbB
C: NAG-NAM(tetrapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6036
Polymers120,1723
Non-polymers4313
Water43224
1
A: L,D-transpeptidase YcbB
C: NAG-NAM(tetrapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6864
Polymers60,3172
Non-polymers3692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase YcbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9172
Polymers59,8551
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.510, 92.558, 276.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 29 - 511 / Label seq-ID: 13 - 495

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein L,D-transpeptidase YcbB


Mass: 59855.277 Da / Num. of mol.: 2
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: Polypeptide(D) NAG-NAM(tetrapeptide)


Mass: 461.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-AMV / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside / [4-({5-amino-3-[(4-cyanophenyl)amino]-1H-1 / 2 / 4-triazole-1-carbonyl}amino)phenoxy]acetic acid / METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucoside / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-D-glucoside / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-glucoside


Type: D-saccharide / Mass: 307.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21NO8 / Source: (synth.) synthetic construct (others) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.29 Å3/Da / Density % sol: 62.56 %
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: 0.97908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.98→48.9 Å / Num. obs: 31171 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.998 / Rpim(I) all: 0.047 / Net I/σ(I): 10
Reflection shellResolution: 2.98→3.14 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 11.5 / Num. unique obs: 4455 / CC1/2: 0.405 / Rpim(I) all: 1.265 / % possible all: 100

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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: 2.98→48.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 27.9 / SU ML: 0.448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1537 4.9 %RANDOM
Rwork0.2095 ---
obs0.2123 29567 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 234.64 Å2 / Biso mean: 114.317 Å2 / Biso min: 51.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---1.18 Å20 Å2
3---0.82 Å2
Refinement stepCycle: final / Resolution: 2.98→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7890 0 60 25 7975
Biso mean--150.11 80.67 -
Num. residues----975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138157
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177593
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.64111120
X-RAY DIFFRACTIONr_angle_other_deg1.1811.58217461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92723.092456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.193151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7021547
X-RAY DIFFRACTIONr_chiral_restr0.0560.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021909
Refine LS restraints NCS

Ens-ID: 1 / Number: 15014 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.98→3.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 117 -
Rwork0.404 2142 -
all-2259 -
obs--100 %

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