[English] 日本語
Yorodumi
- PDB-1ghg: CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ghg
TitleCRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON
ComponentsVANCOMYCIN AGLYCON
KeywordsANTIBIOTIC / GLYCOPEPTIDE / AGLYCON / VANCOMYCIN
Function / homologyVANCOMYCIN AGLYCON / ACETIC ACID / :
Function and homology information
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.98 Å
AuthorsKaplan, J. / Korty, B.D. / Axelsen, P.H. / Loll, P.J.
CitationJournal: J.Med.Chem. / Year: 2001
Title: The Role of Sugar Residues in Molecular Recognition by Vancomycin
Authors: Kaplan, J. / Korty, B.D. / Axelsen, P.H. / Loll, P.J.
History
DepositionDec 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2001Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VANCOMYCIN AGLYCON
B: VANCOMYCIN AGLYCON
C: VANCOMYCIN AGLYCON
D: VANCOMYCIN AGLYCON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,99610
Polymers4,6004
Non-polymers3966
Water1,20767
1
A: VANCOMYCIN AGLYCON
B: VANCOMYCIN AGLYCON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4204
Polymers2,3002
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: VANCOMYCIN AGLYCON
D: VANCOMYCIN AGLYCON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5766
Polymers2,3002
Non-polymers2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.480, 29.480, 74.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-2003-

HOH

-
Components

#1: Protein/peptide
VANCOMYCIN AGLYCON


Type: Oligopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: VANCOMYCIN AGLYCON IS THE NONSUGAR COMPONENT OF VANCOMYCIN, CONSISTING OF THE TRICYCLIC HEPTAPEPTIDE ONLY.
Source: (synth.) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, VANCOMYCIN AGLYCON
#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN AGLYCON IS REPRESENTED BY SEQUENCE (SEQRES)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.87 %
Crystal growpH: 6.9
Details: 100 MM SODIUM CACODYLATE, 1.6 M SODIUM ACETATE, PH 6.9, VAPOR DIFFUSION/HANGING DROP, TEMPERATURE 277K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 %(v/v)DMSO1drop
31.5 Msodium acetate1reservoir
4100 mMsodium cacodylate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 0.98→8 Å / Num. obs: 16377 / % possible obs: 87.2 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.8
Reflection shellResolution: 0.98→1.08 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.238 / % possible all: 66.7

-
Processing

Software
NameClassification
SnBphasing
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 0.98→8 Å / σ(F): 4
Stereochemistry target values: THE FOUR COPIES OF THE MOLECULE IN THE ASYMMETRIC UNIT WERE RESTRAINED TO HAVE SIMLAR 1,2- AND 1,3-DISTANCES. SP2 CENTERS AND RINGS WERE RESTRAINED TO PLANARITY.
Details: CONJUGATE GRADIENT FOR MOST OF REFINEMENT, FOLLOWED BY BLOCKED LEAST SQUARES
RfactorNum. reflection% reflection
Rfree0.15 1422 8.3 %
all0.15 17071 -
obs0.15 -90.9 %
Refinement stepCycle: LAST / Resolution: 0.98→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms320 0 24 67 411
Software
*PLUS
Name: SHELXL / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 8.3 % / Rfactor all: 0.15 / Rfactor Rfree: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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