[English] 日本語
Yorodumi
- PDB-6a6a: VanYB in complex with D-Alanine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a6a
TitleVanYB in complex with D-Alanine
ComponentsD-alanyl-D-alanine carboxypeptidaseMuramoylpentapeptide carboxypeptidase
KeywordsHYDROLASE / Vancomycin resistance / peptidase / metallopeptidase family M15
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / metal ion binding / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D-ALANINE / TRIETHYLENE GLYCOL / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsKim, H.S. / Hahn, H.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning2013R1A2A1A05067303 Korea, Republic Of
Ministry of Science, ICT and Future PlanningNRF-2011-0030001 Korea, Republic Of
Ministry of Science, ICT and Future PlanningNRF-2013M3A6A4043695 Korea, Republic Of
Ministry of Science, ICT and Future PlanningNRF-2017R1C1B2012225 Korea, Republic Of
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB.
Authors: Kim, H.S. / Hahn, H. / Kim, J. / Jang, D.M. / Lee, J.Y. / Back, J.M. / Im, H.N. / Kim, H. / Han, B.W. / Suh, S.W.
History
DepositionJun 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-alanyl-D-alanine carboxypeptidase
B: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,28816
Polymers50,8922
Non-polymers1,39614
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-61 kcal/mol
Surface area16340 Å2
Unit cell
Length a, b, c (Å)85.368, 40.830, 114.672
Angle α, β, γ (deg.)90.00, 109.08, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein D-alanyl-D-alanine carboxypeptidase / Muramoylpentapeptide carboxypeptidase / DD-peptidase


Mass: 25445.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: vanYB, EF_2297 / Production host: Escherichia coli (E. coli)
References: UniProt: Q47746, serine-type D-Ala-D-Ala carboxypeptidase

-
Non-polymers , 6 types, 36 molecules

#2: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 1500, sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 17526 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.1
Reflection shellResolution: 2.29→2.33 Å / Rmerge(I) obs: 0.477 / Num. unique obs: 784

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZHF

5zhf


Resolution: 2.26→36.46 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.616 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 880 5.1 %RANDOM
Rwork0.20159 ---
obs0.20523 16380 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å20.39 Å2
2---0.78 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.26→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 86 22 3049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143083
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172685
X-RAY DIFFRACTIONr_angle_refined_deg1.361.6814165
X-RAY DIFFRACTIONr_angle_other_deg0.9071.6816302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51922.928181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54615492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.681520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023456
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02564
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_it2.2663.3981462
X-RAY DIFFRACTIONr_mcbond_other2.2673.41459
X-RAY DIFFRACTIONr_mcangle_it3.4545.091818
X-RAY DIFFRACTIONr_mcangle_other3.4535.0891819
X-RAY DIFFRACTIONr_scbond_it2.5083.7741619
X-RAY DIFFRACTIONr_scbond_other2.5083.7741619
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9595.5332347
X-RAY DIFFRACTIONr_long_range_B_refined5.66940.5523631
X-RAY DIFFRACTIONr_long_range_B_other5.66840.5613632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.256→2.315 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 42 -
Rwork0.251 765 -
obs--63.54 %

+
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