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- PDB-1hhz: Deglucobalhimycin in complex with cell wall pentapeptide -

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Basic information

Entry
Database: PDB / ID: 1hhz
TitleDeglucobalhimycin in complex with cell wall pentapeptide
Components
  • CELL WALL PEPTIDE
  • DEGLUCOBALHIMYCIN
KeywordsANTIBIOTIC/PEPTIDE / ANTIBIOTIC-PEPTIDE COMPLEX / GLYCOPEPTIDE / ANTIBIOTIC / CELL WALL PEPTIDE / BALHIMYCIN
Function / homologyDeglucobalhimycin / Chem-DVC / R-1,2-PROPANEDIOL / :
Function and homology information
Biological speciesAMYCOLATOPSIS SP. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.99 Å
AuthorsLehmann, C. / Bunkoczi, G. / Sheldrick, G.M. / Vertesy, L.
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
DepositionDec 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2003Provider: 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 / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.3Nov 30, 2012Group: Other
Revision 2.0Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_validate_polymer_linkage / struct_conn
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site ..._chem_comp.type / _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 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jul 24, 2019Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 2.3Oct 9, 2019Group: Data collection / Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn / Item: _pdbx_database_status.status_code_sf
Revision 2.4Jul 29, 2020Group: Advisory / Data collection / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_dist_value ..._chem_comp.type / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEGLUCOBALHIMYCIN
B: DEGLUCOBALHIMYCIN
C: DEGLUCOBALHIMYCIN
D: CELL WALL PEPTIDE
E: CELL WALL PEPTIDE
F: CELL WALL PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,75513
Polymers4,9196
Non-polymers8367
Water1,71195
1
B: DEGLUCOBALHIMYCIN
C: DEGLUCOBALHIMYCIN
E: CELL WALL PEPTIDE
F: CELL WALL PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7868
Polymers3,2794
Non-polymers5074
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6.4 kcal/mol
Surface area3270 Å2
MethodPISA
2
A: DEGLUCOBALHIMYCIN
D: CELL WALL PEPTIDE
hetero molecules

A: DEGLUCOBALHIMYCIN
D: CELL WALL PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,93810
Polymers3,2794
Non-polymers6596
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
Buried area2240 Å2
ΔGint-15.8 kcal/mol
Surface area2280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.290, 48.290, 39.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

21F-2001-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.81806, -0.28248, -0.50097), (0.27498, 0.57294, -0.77209), (0.50513, -0.76938, -0.39103)69.43897, 18.29514, 12.76565
2given(-0.78465, 0.25722, 0.56406), (0.34973, -0.5676, 0.74534), (0.51187, 0.7821, 0.35541)40.4391, -24.31767, -7.14059

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Components

#1: Protein/peptide DEGLUCOBALHIMYCIN


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 1149.977 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: DEGLUCOBALHIMYCIN LACKS THE D-GLUCOSE COMPONENT OF BALHIMYCIN CONSISTING OF THE TRICYCLIC HEPTAPEPTIDE AND (2R,4S,6S)-4-AZANYL-4,6-DIMETHYL-OXANE-2,5,5-TRIOL ONLY LINKED TO RESIDUE 6.
Source: (synth.) AMYCOLATOPSIS SP. (bacteria) / References: NOR: NOR00707, Deglucobalhimycin
#2: Protein/peptide CELL WALL PEPTIDE


Mass: 489.542 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C7H15NO4
Details: DEGLUCOBALHIMYCIN LACKS THE D-GLUCOSE COMPONENT OF BALHIMYCIN CONSISTING OF THE TRICYCLIC HEPTAPEPTIDE AND (2R,4S,6S)-4-AZANYL-4,6-DIMETHYL-OXANE-2,5,5-TRIOL ONLY LINKED TO RESIDUE 6.
References: Deglucobalhimycin
#4: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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, DEGLUCOBALHIMYCIN IS REPRESENTED GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) DVC. GROUP: 1 NAME: DEGLUCOBALHIMYCIN CHAIN: A, B, C COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7 COMPONENT_2: SUGAR RESIDUES 9 DESCRIPTION: DEGLUCOBALHIMYCIN LACKS THE D-GLUCOSE COMPONENT OF BALHIMYCIN CONSISTING OF THE TRICYCLIC HEPTAPEPTIDE AND 4-OXO-VANCOSAMINE ONLY, LINKED TO RESIDUE 6.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 38.1 %
Crystal growpH: 7 / Details: 0.3M CIT, PH=7, 30% 1,2-PROPANEDIOL, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9114
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9114 Å / Relative weight: 1
ReflectionResolution: 0.99→41.85 Å / Num. obs: 29932 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 0.99→1.1 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.19 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.99→41.85 Å / Num. parameters: 4237 / Num. restraintsaints: 4905 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1403 1529 5.1 %SHELLS
all0.1083 29932 --
obs0.1075 -99.9 %-
Solvent computationSolvent model: METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 280.8 / Occupancy sum non hydrogen: 448.5
Refinement stepCycle: LAST / Resolution: 0.99→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms320 0 53 95 468
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0.027
X-RAY DIFFRACTIONs_from_restr_planes0.086
X-RAY DIFFRACTIONs_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.19
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.085
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0.126

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