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- PDB-1lbu: HYDROLASE METALLO (ZN) DD-PEPTIDASE -

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Basic information

Entry
Database: PDB / ID: 1lbu
TitleHYDROLASE METALLO (ZN) DD-PEPTIDASE
ComponentsMURAMOYL-PENTAPEPTIDE CARBOXYPEPTIDASE
KeywordsHYDROLASE / NUCLEAR RECEPTOR / CARBOXYPEPTIDASE
Function / homology
Function and homology information


zinc D-Ala-D-Ala carboxypeptidase / zinc D-Ala-D-Ala carboxypeptidase activity / cell wall organization / extracellular region / metal ion binding
Similarity search - Function
Peptidase M15A, C-terminal / Peptidase M15 / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / PGBD superfamily / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain ...Peptidase M15A, C-terminal / Peptidase M15 / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / PGBD superfamily / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Zinc D-Ala-D-Ala carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsCharlier, P. / Wery, J.-P. / Dideberg, O. / Frere, J.-M.
Citation
Journal: Handbook of Metalloproteins / Year: 2004
Title: Streptomyces Albus G D-Ala-A-Ala Carboxypeptidase
Authors: Charlier, P. / Wery, J.-P. / Dideberg, O. / Frere, J.-M.
#1: Journal: FEBS Lett. / Year: 1994
Title: Binding Site-Shaped Repeated Sequences of Bacterial Wall Peptidoglycan Hydrolases
Authors: Ghuysen, J.M. / Lamotte-Brasseur, J. / Joris, B. / Shockman, G.D.
#2: Journal: Nature / Year: 1982
Title: Structure of a Zn2+-Containing D-Alanyl-D-Alanine-Cleaving Carboxypeptidase at 2.5 A Resolution
Authors: Dideberg, O. / Charlier, P. / Dive, G. / Joris, B. / Frere, J.M. / Ghuysen, J.M.
History
DepositionMar 16, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MURAMOYL-PENTAPEPTIDE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2502
Polymers22,1841
Non-polymers651
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.080, 49.700, 38.650
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MURAMOYL-PENTAPEPTIDE CARBOXYPEPTIDASE


Mass: 22184.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces albus (bacteria) / Strain: G / References: UniProt: P00733, EC: 3.4.17.8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMURAMOYL-PENTAPEPTIDE CARBOXYPEPTIDASE HYDROLYSES INSOLUBLE PEPTIDOGLYCAN CLEAVAGE OF UDP-N- ...MURAMOYL-PENTAPEPTIDE CARBOXYPEPTIDASE HYDROLYSES INSOLUBLE PEPTIDOGLYCAN CLEAVAGE OF UDP-N-ACETYLMURAMOYL-L-ALANYL-D- GAMMA-GLUTAMYL-CARBOXY-L-LYSYL-D-ALANYL-|-D-ALANINE.
Sequence detailsTHE FIRST AMINO ACID OF THE NATIVE PROTEIN IS ASP 1 WHICH IS PARTIALLY BLOCKED IN THIS STRUCTURE AS ...THE FIRST AMINO ACID OF THE NATIVE PROTEIN IS ASP 1 WHICH IS PARTIALLY BLOCKED IN THIS STRUCTURE AS A RESULT OF THE CYCLIZATION OF THE FIRST TWO AMINO ACIDS INTO ANHYDROASPARTYLGLYCINE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 15460 / % possible obs: 100 % / Observed criterion σ(I): 0

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å / σ(F): 2
Details: AMINO ACIDS 43 - 109 ARE SIMILAR TO AMINO ACIDS 194 - 261 OF B. SUBTILIS AUTOLYSIN.
RfactorNum. reflection% reflection
Rwork0.164 --
obs-12633 84 %
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 1 229 1785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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