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- PDB-1hhy: Deglucobalhimycin in complex with D-Ala-D-Ala -

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Basic information

Entry
Database: PDB / ID: 1hhy
TitleDeglucobalhimycin in complex with D-Ala-D-Ala
ComponentsDEGLUCOBALHIMYCIN
KeywordsANTIBIOTIC / GLYCOPEPTIDE / CELL WALL PEPTIDE
Function / homologyDeglucobalhimycin / D-ALANINE / Chem-DVC / S-1,2-PROPANEDIOL / :
Function and homology information
Biological speciesAMYCOLATOPSIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.89 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: 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 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.status_code_sf ..._chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEGLUCOBALHIMYCIN
B: DEGLUCOBALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,13311
Polymers2,3002
Non-polymers8339
Water95553
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-10.4 kcal/mol
Surface area2090 Å2
MethodPISA
2
A: DEGLUCOBALHIMYCIN
hetero molecules

A: DEGLUCOBALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,05710
Polymers2,3002
Non-polymers7578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
Buried area880 Å2
ΔGint-31.8 kcal/mol
Surface area1920 Å2
MethodPISA
3
A: DEGLUCOBALHIMYCIN
B: DEGLUCOBALHIMYCIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)18,79766
Polymers13,80012
Non-polymers4,99754
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation11_556-x+y,y,-z+3/21
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation12_566x,x-y+1,-z+3/21
Buried area11060 Å2
ΔGint-232.8 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.444, 48.444, 43.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-1002-

NA

21A-2005-

HOH

31B-2010-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.30986, -0.75863, -0.57312), (-0.76062, -0.55947, 0.32932), (-0.57047, 0.33388, -0.75039)
Vector: 37.06617, 35.15608, 37.5999)

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Components

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Protein/peptide / Sugars , 2 types, 4 molecules AB

#1: Protein/peptide DEGLUCOBALHIMYCIN


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 1149.977 Da / Num. of mol.: 2 / 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: 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.: 2
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

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Non-polymers , 4 types, 60 molecules

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


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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, DEGLUCOBALHIMYCIN IS REPRESENTED GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) DVC. GROUP: 1 NAME: DEGLUCOBALHIMYCIN CHAIN: A, B 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: 2.4 Å3/Da / Density % sol: 31 %
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: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 0.89→30.06 Å / Num. obs: 22973 / % possible obs: 98.9 % / Redundancy: 7.39 % / Rmerge(I) obs: 0.0298 / Net I/σ(I): 62.93
Reflection shellResolution: 0.89→1 Å / Redundancy: 7.45 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 28.95 / % possible all: 98

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.89→30.06 Å / Num. parameters: 2450 / Num. restraintsaints: 2978 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1394 1127 5 %SHELLS
all0.1217 22768 --
obs0.1212 -98.9 %-
Solvent computationSolvent model: METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 156 / Occupancy sum non hydrogen: 261.13
Refinement stepCycle: LAST / Resolution: 0.89→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms160 0 51 53 264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.096
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.06
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.008
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.024
X-RAY DIFFRACTIONs_approx_iso_adps0.112

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