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- PDB-4ox3: Structure of the LdcB LD-carboxypeptidase reveals the molecular b... -

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Basic information

Entry
Database: PDB / ID: 4ox3
TitleStructure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
ComponentsPutative carboxypeptidase YodJ
KeywordsHYDROLASE / LAS family / LD-carboxypeptidase / Cell wall modifying enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / carboxypeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Peptidase M15B / : / D-alanyl-D-alanine carboxypeptidase / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Putative carboxypeptidase YodJ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHoyland, C.N. / Aldridge, C. / Cleverley, R.M. / Sidiq, K. / Duchene, M.C. / Daniel, R.A. / Vollmer, W. / Lewis, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Structure / Year: 2014
Title: Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition.
Authors: Hoyland, C.N. / Aldridge, C. / Cleverley, R.M. / Duchene, M.C. / Minasov, G. / Onopriyenko, O. / Sidiq, K. / Stogios, P.J. / Anderson, W.F. / Daniel, R.A. / Savchenko, A. / Vollmer, W. / Lewis, R.J.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative carboxypeptidase YodJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4243
Polymers25,2631
Non-polymers1602
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.644, 53.695, 102.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative carboxypeptidase YodJ


Mass: 25263.318 Da / Num. of mol.: 1 / Fragment: UNP residues 61-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU19620,YodJ,yodJ,yokZ / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: O34866, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M phosphate/citrate buffer, pH 4.2, 40 % PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.7→51.17 Å / Num. obs: 25369 / % possible obs: 95.7 % / Redundancy: 3.2 % / Net I/σ(I): 11.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.7 % / % possible all: 89.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→51.17 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.86 / SU B: 4.964 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25137 812 5.2 %RANDOM
Rwork0.20469 ---
obs0.20715 14932 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0 Å2
2--1.05 Å2-0 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 2→51.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 6 160 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021795
X-RAY DIFFRACTIONr_bond_other_d0.0010.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.9672408
X-RAY DIFFRACTIONr_angle_other_deg0.8233883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98725.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35915329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.293158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02405
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.292854
X-RAY DIFFRACTIONr_mcbond_other1.0431.29853
X-RAY DIFFRACTIONr_mcangle_it1.6621.931064
X-RAY DIFFRACTIONr_mcangle_other1.6621.9311065
X-RAY DIFFRACTIONr_scbond_it1.71.501941
X-RAY DIFFRACTIONr_scbond_other1.621.49932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6172.1431333
X-RAY DIFFRACTIONr_long_range_B_refined5.03411.2022280
X-RAY DIFFRACTIONr_long_range_B_other4.78410.8382216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 58 -
Rwork0.197 1057 -
obs--93.07 %

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