[English] 日本語
Yorodumi
- PDB-1go6: Balhimycin in complex with Lys-D-ala-D-ala -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1go6
TitleBalhimycin in complex with Lys-D-ala-D-ala
Components
  • BALHIMYCIN
  • PEPTIDE LYS-DAL-DAL
KeywordsANTIBIOTIC/PEPTIDE / GLYCOPEPTIDE / ANTIBIOTICS / ANTIBIOTIC-PEPTIDE COMPLEX / BACTERIAL CELL-WALL
Function / homologyBalhimycin / beta-D-glucopyranose / CITRIC ACID / Chem-DVC / :
Function and homology information
Biological speciesAMYCOLATOPSIS SP. (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.98 Å
AuthorsLehmann, C. / Bunkoczi, G. / Vertesy, L. / Sheldrick, G.M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structures of Glycopeptide Antibiotics with Peptides that Model Bacterial Cell-Wall Precursors
Authors: Lehmann, C. / Bunkoczi, G. / Vertesy, L. / Sheldrick, G.M.
History
DepositionOct 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Jul 25, 2012Group: Atomic model / Non-polymer description / Other
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4Feb 27, 2013Group: Derived calculations
Revision 1.5Mar 20, 2013Group: Derived calculations
Revision 1.6Feb 8, 2017Group: Source and taxonomy
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.5Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BALHIMYCIN
B: PEPTIDE LYS-DAL-DAL
C: BALHIMYCIN
D: PEPTIDE LYS-DAL-DAL
E: BALHIMYCIN
F: PEPTIDE LYS-DAL-DAL
G: BALHIMYCIN
H: PEPTIDE LYS-DAL-DAL
I: BALHIMYCIN
K: BALHIMYCIN
M: BALHIMYCIN
O: BALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,41335
Polymers10,35712
Non-polymers4,05623
Water4,666259
1
A: BALHIMYCIN
B: PEPTIDE LYS-DAL-DAL
C: BALHIMYCIN
D: PEPTIDE LYS-DAL-DAL
I: BALHIMYCIN
K: BALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,22918
Polymers5,1796
Non-polymers2,05012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-42.4 kcal/mol
Surface area6660 Å2
MethodPISA
2
M: BALHIMYCIN
O: BALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3998
Polymers2,3002
Non-polymers1,0996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-3.3 kcal/mol
Surface area2110 Å2
MethodPISA
3
E: BALHIMYCIN
F: PEPTIDE LYS-DAL-DAL
G: BALHIMYCIN
H: PEPTIDE LYS-DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7859
Polymers2,8794
Non-polymers9075
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-9.2 kcal/mol
Surface area3080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.927, 28.025, 50.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9819, 0.18938, 0.00116), (0.18938, -0.9819, 0.00173), (0.00146, -0.00148, -1)-1.10154, 10.82174, 76.56329
2given(-0.73596, 0.64486, -0.20617), (-0.67696, -0.69685, 0.23691), (0.0091, 0.31393, 0.9494)131.91583, 61.36913, 7.03697
3given(-0.60778, -0.76943, 0.19645), (-0.79125, 0.56579, -0.23198), (0.06734, -0.29643, -0.95268)124.77338, 71.83916, 83.28141
4given(0.0734, 0.99339, -0.08829), (0.99491, -0.07907, -0.06249), (-0.06906, -0.08326, -0.99413)64.14457, -61.33841, 102.40584
5given(0.27739, -0.95464, 0.10828), (0.95595, 0.2855, 0.06815), (-0.09597, 0.08461, 0.99178)66.03882, -67.88586, 26.25597
6given(0.61084, -0.78998, 0.05292), (0.78383, 0.61281, 0.10043), (-0.11177, -0.01986, 0.99354)63.37468, -51.10247, 17.46341
7given(0.82123, 0.57059, -0.00089), (0.56936, -0.81956, -0.06448), (-0.03752, 0.05244, -0.99792)17.46895, 5.25723, 86.4636

-
Components

-
Protein/peptide , 2 types, 12 molecules ACEGIKMOBDFH

#1: Protein/peptide
BALHIMYCIN


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 1149.977 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: BALHIMYCIN IS A TRICYCLIC HEPTAPEPTIDE GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4 AND BY 4-OXO-VANCOSAMINE (RESIDUE 9) ON RESIDUE 6.
Source: (natural) AMYCOLATOPSIS SP. (bacteria) / Strain: Y-86, 21022 / References: NOR: NOR00709, Balhimycin
#2: Protein/peptide
PEPTIDE LYS-DAL-DAL


Mass: 289.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Sugars , 2 types, 16 molecules

#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
Details: BALHIMYCIN IS A TRICYCLIC HEPTAPEPTIDE GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4 AND BY 4-OXO-VANCOSAMINE (RESIDUE 9) ON RESIDUE 6.
References: Balhimycin
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-DVC / (2R,4S,6S)-4-azanyl-4,6-dimethyl-oxane-2,5,5-triol


Type: L-saccharide, alpha linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 177.198 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C7H15NO4
Details: BALHIMYCIN IS A TRICYCLIC HEPTAPEPTIDE GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4 AND BY 4-OXO-VANCOSAMINE (RESIDUE 9) ON RESIDUE 6.
References: Balhimycin

-
Non-polymers , 4 types, 266 molecules

#5: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsBALHIMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...BALHIMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY TWO MONOSACCHARIDES: A D-GLUCOSE AND A 4-OXO-VANCOSAMINE. HERE, BALHIMYCIN IS REPRESENTED GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) DVC AND BGC GROUP: 1 NAME: BALHIMYCIN CHAIN: A, C, E, G, I, K, M, O COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7 COMPONENT_2: SUGAR RESIDUES 8 AND 9 DESCRIPTION: BALHIMYCIN IS A TRICYCLIC HEPTAPEPTIDE GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4 AND BY 4-OXO-VANCOSAMINE (RESIDUE 9) ON RESIDUE 6.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 %
Description: ADDITIONAL DATA SET WAS COLLECTED AT CU KALPHA RADIATION
Crystal growpH: 4 / Details: 0.3 M NA3CIT/H3CIT PH=4, 25% MPD, pH 4.00
Crystal grow
*PLUS
Temperature: 291 K / pH: 4 / Method: vapor diffusion, hanging drop / Details: Loll, P.J., (1999) J.Med.Chem., 42, 4714.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
20.3 MNa3Cit/H3Cit1reservoir
325 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 0.98→90 Å / Num. obs: 72913 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.81
Reflection shellResolution: 0.98→1.1 Å / Rmerge(I) obs: 0.1774 / Mean I/σ(I) obs: 6.72 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 90 Å / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Lowest resolution: 1.1 Å / % possible obs: 95.5 %

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 0.98→89 Å / Num. parameters: 12104 / Num. restraintsaints: 16491 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: RESTRAINTS FOR BALHIMYCIN FROM CSD
Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1592 3629 5 %THIN SHELLS
all0.1303 72913 --
obs0.1288 -98.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeOccupancy sum hydrogen: 728.86 / Occupancy sum non hydrogen: 1106.67
Refinement stepCycle: LAST / Resolution: 0.98→89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 246 259 1225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.045
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.096
X-RAY DIFFRACTIONs_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.063
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.029
X-RAY DIFFRACTIONs_approx_iso_adps0.082
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1254 / Rfactor Rfree: 0.1542 / Rfactor Rwork: 0.1254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.096
X-RAY DIFFRACTIONs_chiral_restr0.097

+
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