[English] 日本語
Yorodumi
- PDB-2vgk: Crystal structure of Actinomadura R39 DD-peptidase complexed with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vgk
TitleCrystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASEMuramoylpentapeptide carboxypeptidase
KeywordsHYDROLASE / CELL WALL BIOGENESIS/DEGRADATION / ANTIBIOTIC RESISTANCE / PEPTIDOGLYCAN SYNTHESIS / PROTEASE / SECRETED / CELL SHAPE / CARBOXYPEPTIDASE / PENICILLIN-BINDING / ACTINOMADURA / PEPTIDOGLYCAN / TRANSPEPTIDASE
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region
Similarity search - Function
D-Ala-D-Ala carboxypeptidase C, peptidase S13 / Peptidase S13, D-Ala-D-Ala carboxypeptidase C / D-Ala-D-Ala carboxypeptidase 3 (S13) family / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(bba) Sandwich / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-REZ / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesACTINOMADURA SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSauvage, E. / kerff, F. / Herman, R. / Charlier, P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structures of Complexes of Bacterial Dd-Peptidases with Peptidoglycan-Mimetic Ligands: The Substrate Specificity Puzzle.
Authors: Sauvage, E. / Powell, A.J. / Heilemann, J. / Josephin, H.R. / Charlier, P. / Davies, C. / Pratt, R.F.
History
DepositionNov 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,09331
Polymers200,3354
Non-polymers2,75727
Water8,917495
1
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8599
Polymers50,0841
Non-polymers7758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8107
Polymers50,0841
Non-polymers7276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8107
Polymers50,0841
Non-polymers7276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6138
Polymers50,0841
Non-polymers5297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.140, 93.350, 109.100
Angle α, β, γ (deg.)90.00, 94.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / Muramoylpentapeptide carboxypeptidase / DD-PEPTIDASE / DD-CARBOXYPEPTIDASE


Mass: 50083.812 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP. (bacteria) / Strain: R39
References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-REZ / (2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID


Mass: 246.260 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18N2O5
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.3 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 99513 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W79

1w79


Resolution: 2.25→15.71 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.867 / SU B: 9.762 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 4989 5 %RANDOM
Rwork0.23 ---
obs0.233 94249 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→15.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13394 0 155 495 14044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113758
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.97318828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88451858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.425.47574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.694151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.51568
X-RAY DIFFRACTIONr_chiral_restr0.0760.22176
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210663
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.24700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.28943
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4361.59398
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.736214556
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0434911
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6694.54272
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.3 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.415 321
Rwork0.368 6201

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more