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- PDB-4ox5: Structure of the LdcB LD-carboxypeptidase reveals the molecular b... -

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Basic information

Entry
Database: PDB / ID: 4ox5
TitleStructure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
ComponentsLdcB LD-carboxypeptidase
KeywordsHYDROLASE / LAS family / LD-carboxypeptidase / Cell wall modifying enzyme
Function / homology
Function and homology information


peptidase activity / proteolysis / metal ion binding
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
D-ALANINE / Peptidase M15B domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_keywords
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_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / refine_hist / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_conn.ptnr2_symmetry
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LdcB LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8988
Polymers21,3371
Non-polymers5617
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LdcB LD-carboxypeptidase
hetero molecules

A: LdcB LD-carboxypeptidase
hetero molecules

A: LdcB LD-carboxypeptidase
hetero molecules

A: LdcB LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,59232
Polymers85,3484
Non-polymers2,24428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6310 Å2
ΔGint-477 kcal/mol
Surface area34180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.855, 60.414, 138.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-425-

HOH

31A-468-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LdcB LD-carboxypeptidase


Mass: 21336.930 Da / Num. of mol.: 1 / Fragment: UNP residues 56-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr0554 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8DQQ1

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Non-polymers , 6 types, 205 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M mixture of amino acids (glycine, L-glutamate, and racemates of alanine, serine and lysine), 0.1 M buffer system 2, pH 7.5 and 37.5 % MPD/PEG1000/PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→19.95 Å / Num. obs: 25656 / % possible obs: 98.6 % / Redundancy: 24.3 % / Net I/σ(I): 34.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 2.4 / % possible all: 86.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.949 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.944 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25147 955 5 %RANDOM
Rwork0.19058 ---
obs0.1933 18174 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.116 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----2.73 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 26 198 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191538
X-RAY DIFFRACTIONr_bond_other_d0.0010.021382
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.9682063
X-RAY DIFFRACTIONr_angle_other_deg0.83933186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33624.8179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99915237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.804155
X-RAY DIFFRACTIONr_chiral_restr0.2490.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
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_it3.7313.947742
X-RAY DIFFRACTIONr_mcbond_other3.7123.945740
X-RAY DIFFRACTIONr_mcangle_it4.7645.891921
X-RAY DIFFRACTIONr_mcangle_other4.7625.894922
X-RAY DIFFRACTIONr_scbond_it4.6264.365796
X-RAY DIFFRACTIONr_scbond_other4.6234.371797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0536.4221143
X-RAY DIFFRACTIONr_long_range_B_refined12.19834.5742020
X-RAY DIFFRACTIONr_long_range_B_other12.19634.5992021
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 62 -
Rwork0.331 1157 -
obs--86.52 %

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