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

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Basic information

Entry
Database: PDB / ID: 4oxd
TitleStructure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
Components
  • LdcB LD-carboxypeptidase
  • MUB-ALA-ZGL-LYS-DSG
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
LYSINE / N-acetyl-alpha-muramic acid / Peptidase M15B domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
Lactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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 5, 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 1.3Jan 7, 2015Group: Database references
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_keywords / symmetry
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.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 / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_id / _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.value / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _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.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 3.0Apr 10, 2024Group: 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_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can ..._entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LdcB LD-carboxypeptidase
B: LdcB LD-carboxypeptidase
C: LdcB LD-carboxypeptidase
D: LdcB LD-carboxypeptidase
E: LdcB LD-carboxypeptidase
H: MUB-ALA-ZGL-LYS-DSG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,15529
Polymers106,4426
Non-polymers1,71323
Water2,000111
1
A: LdcB LD-carboxypeptidase
H: MUB-ALA-ZGL-LYS-DSG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1717
Polymers21,6572
Non-polymers5145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LdcB LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7368
Polymers21,1961
Non-polymers5407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LdcB LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4936
Polymers21,1961
Non-polymers2975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LdcB LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3634
Polymers21,1961
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: LdcB LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3924
Polymers21,1961
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)345.954, 42.549, 79.318
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

ZN

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Components

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Protein / Protein/peptide / Sugars , 3 types, 7 molecules ABCDEH

#1: Protein
LdcB LD-carboxypeptidase


Mass: 21196.246 Da / Num. of mol.: 5 / Fragment: UNP residues 56-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Strain: R6 / Gene: spr0554 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8DQQ1
#2: Protein/peptide MUB-ALA-ZGL-LYS-DSG


Mass: 460.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lactobacillus acidophilus (bacteria)
#7: Sugar ChemComp-MUB / N-acetyl-alpha-muramic acid / N-acetyl-muramic acid / N-ACETYLMURAMIC ACID


Type: D-saccharide, alpha linking / Mass: 293.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO8
IdentifierTypeProgram
a-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 133 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHERE IS A NON-STANDARD LINKAGE IN CHAIN H BETWEEN LYS 4 AND DSC 5 THROUGH NZ ATOM OF LYS AND C ATOM OF DSG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium chloride, 0.1 M Hepes pH 8, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.8→47.8 Å / Num. obs: 47327 / % possible obs: 98.3 % / Redundancy: 3.4 % / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / % possible all: 98.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.8→47.8 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.809 / SU B: 22.531 / SU ML: 0.443 / Cross valid method: THROUGHOUT / ESU R Free: 0.495 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1457 5.1 %RANDOM
Rwork0.273 ---
obs0.276 27113 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å21.22 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7065 0 31 111 7207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197290
X-RAY DIFFRACTIONr_bond_other_d0.0080.026506
X-RAY DIFFRACTIONr_angle_refined_deg0.8421.9569779
X-RAY DIFFRACTIONr_angle_other_deg0.677315047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7945864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41624.841378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.447151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2761523
X-RAY DIFFRACTIONr_chiral_restr0.0480.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028292
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021688
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_it0.9524.423503
X-RAY DIFFRACTIONr_mcbond_other0.9524.423502
X-RAY DIFFRACTIONr_mcangle_it1.7026.6164352
X-RAY DIFFRACTIONr_mcangle_other1.7026.6164353
X-RAY DIFFRACTIONr_scbond_it0.7984.4843783
X-RAY DIFFRACTIONr_scbond_other0.7984.4843783
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3126.6995427
X-RAY DIFFRACTIONr_long_range_B_refined3.64935.2268195
X-RAY DIFFRACTIONr_long_range_B_other3.64935.2268196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 108 -
Rwork0.329 1979 -
obs--98.35 %

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