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- PDB-1hhc: Crystal structure of Decaplanin - space group P21, second form -

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Basic information

Entry
Database: PDB / ID: 1hhc
TitleCrystal structure of Decaplanin - space group P21, second form
ComponentsDECAPLANIN
KeywordsANTIBIOTIC / GLYCOPEPTIDE
Function / homologyDecaplanin / CITRIC ACID / 4-epi-vancosamine / :
Function and homology information
Biological speciesUNCULTURED ACTINOMYCETE (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.13 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 22, 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 25, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description
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: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _diffrn_source.pdbx_synchrotron_y_n / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_y_n / _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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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.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_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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 3.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._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

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)6,98815
Polymers4,4624
Non-polymers2,52611
Water2,936163
1
A: DECAPLANIN
B: DECAPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3987
Polymers2,2312
Non-polymers1,1675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: DECAPLANIN
D: DECAPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5908
Polymers2,2312
Non-polymers1,3596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.945, 31.908, 34.735
Angle α, β, γ (deg.)90.00, 109.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96665, -0.17888, -0.1833), (-0.14004, -0.23007, 0.96305), (-0.21444, 0.95659, 0.19735)0.07411, -26.26217, 20.64583
2given(0.76113, 0.00413, 0.64858), (-0.03565, -0.9982, 0.04819), (0.64761, -0.0598, -0.75962)-14.32841, 12.11362, 40.40091
3given(-0.85129, 0.24666, -0.46311), (0.50215, 0.12703, -0.8554), (-0.15217, -0.96074, -0.232)3.44473, 12.69141, 43.50352

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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 HIL 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. HERE, DECAPLSNIN IS REPRESENTED BY GROUPING TOGETGHER THE ...DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. HERE, DECAPLSNIN IS REPRESENTED BY GROUPING TOGETGHER 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 BY A MONOSACCHARIDE AND A DISACCHARIDE

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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: 48.11 %
Crystal growpH: 7 / Details: 1M NA3CIT PH=7.0, PH 7.00

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SEALED TUBE / Type: SIEMENS-STOE-HUBER / Wavelength: 0.71073
DetectorType: SIEMENS / Detector: CCD / Date: Dec 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71073 Å / Relative weight: 1
ReflectionResolution: 1.13→18.08 Å / Num. obs: 20450 / % possible obs: 96.8 % / Redundancy: 7.14 % / Rmerge(I) obs: 0.0981 / Net I/σ(I): 12.34
Reflection shellResolution: 1.13→1.25 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.67 / % possible all: 88.2

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Processing

Software
NameClassification
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HH3

1hh3


Resolution: 1.13→18.08 Å / Num. parameters: 5685 / Num. restraintsaints: 1007 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1901 4.9 %SHELLS
all0.2242 38893 --
obs0.2221 -96.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum non hydrogen: 623.5
Refinement stepCycle: LAST / Resolution: 1.13→18.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms313 0 153 163 629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.042
X-RAY DIFFRACTIONs_angle_d0.041
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.076
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.146
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.014
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.011
X-RAY DIFFRACTIONs_approx_iso_adps0.084

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