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- PDB-2l65: HADDOCK calculated model of the complex of the resistance protein... -

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Basic information

Entry
Database: PDB / ID: 2l65
TitleHADDOCK calculated model of the complex of the resistance protein CalC and Calicheamicin-Gamma
ComponentsCalC
KeywordsStructural genomics / Unknown function / Resistance Protein / PSI-1 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,6-dideoxy-4-thio-beta-D-allopyranose / Chem-HIB / 3-O-methyl-alpha-L-rhamnopyranose / Chem-MTC / CalC
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSingh, S. / Markley, J.L. / Thorson, J.S. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acs Chem.Biol. / Year: 2006
Title: Structural insight into the self-sacrifice mechanism of enediyne resistance.
Authors: Singh, S. / Hager, M.H. / Zhang, C. / Griffith, B.R. / Lee, M.S. / Hallenga, K. / Markley, J.L. / Thorson, J.S.
History
DepositionNov 15, 2010Deposition site: BMRB / Processing site: RCSB
SupersessionMar 2, 2011ID: 2GKC
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3236
Polymers17,9151
Non-polymers1,4085
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CalC


Mass: 17915.072 Da / Num. of mol.: 1 / Fragment: sequence database residues 27-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KNF0

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 2,4-dideoxy-4-(ethylamino)-3-O-methyl-alpha-L-threo-pentopyranose-(1-2)-4-amino-4,6-dideoxy-beta-D- ...2,4-dideoxy-4-(ethylamino)-3-O-methyl-alpha-L-threo-pentopyranose-(1-2)-4-amino-4,6-dideoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 320.382 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122m-1b_1-5_4*N][ad21h-1a_1-5_3*OC_4*NCC]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-6-deoxy-Glcp4N]{[(2+1)][a-L-2-deoxy-Xylp3Me4N]{[(4+1)][ethyl]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-DSR / 2,6-dideoxy-4-thio-beta-D-allopyranose / 2,6-dideoxy-4-thio-beta-D-allose / 2,6-dideoxy-4-thio-D-allose / 2,6-dideoxy-4-thio-allose


Type: D-saccharide, beta linking / Mass: 164.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O3S
IdentifierTypeProgram
b-D-2,6-deoxy-Allp4SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Sugar ChemComp-MRP / 3-O-methyl-alpha-L-rhamnopyranose / 3-O-METHYL-ALPHA-L-RHAMNOPYRANOSIDE / 6-deoxy-3-O-methyl-alpha-L-mannopyranose / 3-O-methyl-alpha-L-rhamnose / 3-O-methyl-L-rhamnose / 3-O-methyl-rhamnose


Type: L-saccharide, alpha linking / Mass: 178.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O5
IdentifierTypeProgram
a-L-Rhap3OMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 2 molecules

#4: Chemical ChemComp-HIB / 4-HYDROXY-5-IODO-2,3-DIMETHOXY-6-METHYLBENZOIC ACID


Mass: 338.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11IO5
#6: Chemical ChemComp-MTC / [1,8-DIHYDROXY-11-OXO-13-(2-METHYLTRITHIO-ETHYLIDENE)-BICYCLO[7.3.1]TRIDECA-4,9-DIENE-2,6-DIYN-10-YL]-CARBAMIC ACID METHYL ESTER


Mass: 407.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17NO4S3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC
NMR detailsText: Chemical Shift Perturbation

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Sample preparation

DetailsContents: 0.5 mM [U-100% 15N] CalC, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.5 mM / Component: CalC-1 / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 150mM / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK2.1Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinstructure solution
HADDOCK2.1Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURE OF THE COMPLEX WAS DETERMINED WITH HADDOCK USING 26 AMBIGUOUS INTERACTION RESTRAINTS DERIVED FROM NMR CHEMICAL SHIFT PERTURBATION DATA AND MUTAGENESIS DATA. THE CHEMICAL SHIFT ...Details: THE STRUCTURE OF THE COMPLEX WAS DETERMINED WITH HADDOCK USING 26 AMBIGUOUS INTERACTION RESTRAINTS DERIVED FROM NMR CHEMICAL SHIFT PERTURBATION DATA AND MUTAGENESIS DATA. THE CHEMICAL SHIFT PERTURBATION DATA WERE OBTAINED BY ANALYSIS OF 1H-15N HSQC SPECTRA RECORDED WITH INCREASING RNA CONCENTRATIONS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 4

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