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- PDB-6d4k: Crystal structure of L,D-transpeptidase 3 from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 6d4k
TitleCrystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution
ComponentsProbable L,D-transpeptidase 3
KeywordsTRANSFERASE / Apo-form
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / extracellular region
Similarity search - Function
Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like ...Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Probable L,D-transpeptidase 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å
AuthorsLibreros, G.A. / Dias, M.V.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/09188-8 Brazil
CitationJournal: ACS Infect Dis / Year: 2019
Title: Structural Basis for the Interaction and Processing of beta-Lactam Antibiotics by l,d-Transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis.
Authors: Libreros-Zuniga, G.A. / Dos Santos Silva, C. / Salgado Ferreira, R. / Dias, M.V.B.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable L,D-transpeptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1212
Polymers28,0811
Non-polymers401
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.122, 46.407, 112.575
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 Probable L,D-transpeptidase 3 / LDT 3 / Ldt(Mt3)


Mass: 28081.379 Da / Num. of mol.: 1 / Fragment: residues 32-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1433, RVBD_1433, P425_01489 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O06825, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000 10% (w/v), Hepes 100 mM, calcium acetate 200 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→46.41 Å / Num. obs: 54013 / % possible obs: 98.1 % / Redundancy: 12.3 % / Biso Wilson estimate: 18.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Net I/σ(I): 21.8 / Num. measured all: 667060 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.32-1.3413.51.24626930.8280.3461.29496.7
7.11-46.4110.10.0444310.9980.0150.04799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.27data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K73

4k73


Resolution: 1.32→42.904 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.69
RfactorNum. reflection% reflection
Rfree0.2178 2575 4.81 %
Rwork0.1756 --
obs0.1776 53565 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.29 Å2 / Biso mean: 34.9071 Å2 / Biso min: 13.94 Å2
Refinement stepCycle: final / Resolution: 1.32→42.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 1 231 2011
Biso mean--16.62 42.73 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051853
X-RAY DIFFRACTIONf_angle_d0.8492552
X-RAY DIFFRACTIONf_chiral_restr0.08289
X-RAY DIFFRACTIONf_plane_restr0.007336
X-RAY DIFFRACTIONf_dihedral_angle_d14.601653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.32-1.34540.31511450.25382757290296
1.3454-1.37290.30481300.25622789291996
1.3729-1.40270.26691670.23282762292996
1.4027-1.43530.26691200.22372775289597
1.4353-1.47120.31621470.26352804295196
1.4712-1.5110.28441390.23092735287495
1.511-1.55550.23781250.17642809293497
1.5555-1.60570.20061390.15862831297097
1.6057-1.66310.21261600.15232802296297
1.6631-1.72970.21181650.15292815298098
1.7297-1.80840.20421430.16062829297298
1.8084-1.90370.28281110.2542725283692
1.9037-2.0230.26541250.23162774289995
2.023-2.17920.20671320.16492902303499
2.1792-2.39850.23671690.18072847301698
2.3985-2.74550.21251630.17182925308899
2.7455-3.45880.20771570.160729653122100
3.4588-42.92710.18431380.15263144328299

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