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- PDB-6d51: Crystal structure of L,D-transpeptidase 3 from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 6d51
TitleCrystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis in complex with a faropenem-derived adduct
ComponentsProbable L,D-transpeptidase 3
KeywordsTRANSFERASE / Adduct
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
Similarity search - Function
Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain ...Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETYL GROUP / Probable L,D-transpeptidase 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 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 19, 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 / struct_conn_type
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0373
Polymers27,9531
Non-polymers842
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.067, 46.175, 110.724
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: 27953.246 Da / Num. of mol.: 1 / Fragment: residues 33-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (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-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE AUTHORS STATE THAT SOME BETA LACTAM ANTIBIOTICS, SUCH AS FAROPENEM, CAN BE PROCESSED OR ...THE AUTHORS STATE THAT SOME BETA LACTAM ANTIBIOTICS, SUCH AS FAROPENEM, CAN BE PROCESSED OR DEGRADED AFTER ACYLATION OF L,D-TRANSPEPTIDASES. THIS ENTRY PRESENT AS A SIMILAR CASE WITH LDTMT1 AND LDTMT2, BUT IN THIS CASE FAROPENEM WAS PROCESSED UNTIL AN ACETYL FRAGMENT THAT REMAINED COVALENTLY LINKED AT CATALYTIC CYSTEINE.

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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: 2.2 Å3/Da / Density % sol: 38.96 %
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: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.83→46.17 Å / Num. obs: 20633 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 26.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Net I/σ(I): 20.4 / Num. measured all: 253996 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.83-1.8712.41.1431532212310.7930.3361.1932.299.4
8.97-46.1710.10.03522302200.9990.0110.03748.198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K73

4k73


Resolution: 1.83→40.944 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.19
RfactorNum. reflection% reflection
Rfree0.239 1020 4.96 %
Rwork0.1944 --
obs0.1966 20565 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.85 Å2 / Biso mean: 37.8167 Å2 / Biso min: 14.88 Å2
Refinement stepCycle: final / Resolution: 1.83→40.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 4 201 1977
Biso mean--47.98 37.66 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071838
X-RAY DIFFRACTIONf_angle_d0.8172523
X-RAY DIFFRACTIONf_chiral_restr0.058284
X-RAY DIFFRACTIONf_plane_restr0.006331
X-RAY DIFFRACTIONf_dihedral_angle_d5.3951467
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.92650.34931550.32222704285999
1.9265-2.04720.26821440.22827232867100
2.0472-2.20530.23241440.203927832927100
2.2053-2.42720.27271510.187827512902100
2.4272-2.77830.2581300.206628082938100
2.7783-3.50010.26871290.191428262955100
3.5001-40.95370.19691670.171729503117100

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