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- PDB-1hhu: Balhimycin in complex with D-Ala-D-Ala -

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Basic information

Entry
Database: PDB / ID: 1hhu
TitleBalhimycin in complex with D-Ala-D-Ala
ComponentsBALHIMYCIN
KeywordsANTIBIOTIC / GLYCOPEPTIDE / CELL WALL PEPTIDES
Function / homologyBalhimycin / beta-D-glucopyranose / CITRIC ACID / D-ALANINE / Chem-DVC / :
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. / Vertessy, 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 28, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Feb 6, 2013Group: Atomic model
Revision 1.5Mar 6, 2013Group: 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 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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
Revision 4.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BALHIMYCIN
B: BALHIMYCIN
C: BALHIMYCIN
D: BALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,93927
Polymers4,6004
Non-polymers3,33923
Water2,252125
1
A: BALHIMYCIN
D: BALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,25815
Polymers2,3002
Non-polymers1,95813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-10.4 kcal/mol
Surface area2470 Å2
MethodPISA
2
B: BALHIMYCIN
C: BALHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,68112
Polymers2,3002
Non-polymers1,38110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-10.6 kcal/mol
Surface area2350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.705, 27.986, 44.490
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96332, -0.04923, 0.26381), (-0.00884, 0.98832, 0.15214), (-0.26822, 0.14423, -0.9525)12.62952, -4.70875, 64.23579
2given(0.99497, -0.00429, 0.10007), (-0.00401, -0.99999, -0.00298), (0.10008, 0.00257, -0.99498)-3.24436, 63.4265, 65.4611
3given(-0.9848, -0.03762, 0.16956), (0.0114, -0.98815, -0.15307), (0.17331, -0.14882, 0.97356)15.83975, 68.02299, 2.86101

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
BALHIMYCIN


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 1149.977 Da / Num. of mol.: 4 / 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) / References: NOR: NOR00709, Balhimycin

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Sugars , 2 types, 8 molecules

#2: 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.: 4
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
#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.: 4
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

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Non-polymers , 4 types, 140 molecules

#4: Chemical
ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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, BALHIMYCIN IS REPRESENTED GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) DVC AND BGC GROUP: 1 NAME: BALHIMYCIN CHAIN: A, B, C, D 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.

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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: 2.14 Å3/Da / Density % sol: 22.4 %
Crystal growpH: 7 / Details: 1M CIT, PH =7, 25% MPD

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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→27.99 Å / Num. obs: 42306 / % possible obs: 99.4 % / Redundancy: 3.66 % / Rmerge(I) obs: 0.0169 / Net I/σ(I): 38.76
Reflection shellResolution: 0.89→1 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.0339 / Mean I/σ(I) obs: 24.67 / % possible all: 98.1

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.89→27.99 Å / Num. parameters: 6200 / Num. restraintsaints: 9467 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: FRIDEL OPPOSITES DURING REFINEMENT NOT MERGED
RfactorNum. reflection% reflectionSelection details
Rfree0.1004 4260 5.2 %SHELLS
all0.0837 82360 --
obs0.0835 -99.4 %-
Solvent computationSolvent model: METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 28 / Occupancy sum hydrogen: 354.5 / Occupancy sum non hydrogen: 630.5
Refinement stepCycle: LAST / Resolution: 0.89→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms320 0 210 125 655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.027
X-RAY DIFFRACTIONs_angle_d0.042
X-RAY DIFFRACTIONs_similar_dist0.017
X-RAY DIFFRACTIONs_from_restr_planes0.107
X-RAY DIFFRACTIONs_zero_chiral_vol0.128
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.082
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.029
X-RAY DIFFRACTIONs_approx_iso_adps0.065

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