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- PDB-1hh3: Decaplanin first P21-Form -

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Basic information

Entry
Database: PDB / ID: 1hh3
TitleDecaplanin first P21-Form
ComponentsDECAPLANIN
KeywordsANTIBIOTIC / GLYCOPEPTIDE
Function / homologyDecaplanin / 4-epi-vancosamine / :
Function and homology information
Biological speciesUNCULTURED ACTINOMYCETE (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1 Å
AuthorsLehmann, C. / Vertessy, L. / Sheldrick, G.M. / Dauter, Z. / Dauter, M.
CitationJournal: Helv.Chim.Acta / Year: 2003
Title: Structures of Four Crystal Forms of Decaplanin
Authors: Lehmann, C. / Debreczeni, J.E. / Bunkoczi, G. / Dauter, M. / Dauter, Z. / Vertesy, L. / Sheldrick, G.M.
History
DepositionDec 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2005Provider: 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 11, 2012Group: Other
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4May 1, 2013Group: Non-polymer description
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._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 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Apr 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,68815
Polymers4,4624
Non-polymers2,22611
Water2,918162
1
A: DECAPLANIN
B: DECAPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3908
Polymers2,2312
Non-polymers1,1596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: DECAPLANIN
D: DECAPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2987
Polymers2,2312
Non-polymers1,0675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.604, 38.598, 31.713
Angle α, β, γ (deg.)90.00, 105.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.91298, -0.04233, -0.4058), (-0.07092, -0.963, 0.26002), (-0.40179, 0.26617, 0.8762)21.28236, 8.5914, 3.72184
2given(-0.94357, -0.32931, -0.03507), (-0.33035, 0.9285, 0.1696), (-0.02329, 0.17161, -0.98489)33.79558, 1.72432, -6.57555
3given(0.8997, 0.34158, 0.27179), (0.17327, -0.85093, 0.49588), (0.40065, -0.39905, -0.82477)10.61809, 3.4368, -9.36413

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Components

#1: Protein/peptide
DECAPLANIN / M86-1410


Type: Glycopeptide / Class: Antibiotic / Mass: 1115.532 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: CULTURE Y-86, 36910
Source: (natural) UNCULTURED ACTINOMYCETE (environmental samples)
Strain: DSM 4763 / References: NOR: NOR00692, Decaplanin
#2: Polysaccharide
alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide, Glycopeptide / Class: Antibiotic / Mass: 326.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L, GLYCOSYLATED
References: Decaplanin
DescriptorTypeProgram
LRhapa1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2211m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-ERE / 4-epi-vancosamine / (1R,3S,4R,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose


Type: L-saccharide, alpha linking, Glycopeptide / Class: Antibiotic / Mass: 161.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H15NO3
Details: DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L, GLYCOSYLATED
References: Decaplanin
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. HERE, DECAPLSNIN IS REPRESENTED BY GROUPING TOGETHER THE ...DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. HERE, DECAPLSNIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE THREE LIGANDS (HET) BGC, ERE AND RAM. GROUP: 1 NAME: DECAPLANIN CHAIN: A, B, C, D COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7 COMPONENT_2: SUGAR RESIDUES 8, 9 AND 10 DESCRIPTION: DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L, GLYCOSYLATED
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 51.9 %
Crystal growpH: 8.5 / Details: 39% LI2SO4, 0.2M TRIS 8.5, 20% GLYCEROL, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: CHESS / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1→30.5 Å / Num. obs: 32325 / % possible obs: 98.5 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.22
Reflection shellResolution: 1→1.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 4.45 / % possible all: 96.2

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1→30.5 Å / Num. parameters: 5659 / Num. restraintsaints: 7613 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1478 1535 4.83 %SHELLS
all0.1159 31754 --
obs0.1148 -98.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 352.2 / Occupancy sum non hydrogen: 150.9
Refinement stepCycle: LAST / Resolution: 1→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms311 0 142 162 615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes0.091
X-RAY DIFFRACTIONs_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.059
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.028
X-RAY DIFFRACTIONs_approx_iso_adps0.119

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