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- PDB-1j5i: Solution Structure of a Novel Chromoprotein Derived from Apo-Neoc... -

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Basic information

Entry
Database: PDB / ID: 1j5i
TitleSolution Structure of a Novel Chromoprotein Derived from Apo-Neocarzinostatin and a Synthetic Chromophore
ComponentsPROTEIN (Apo-Neocarzinostatin)
KeywordsANTIBIOTIC / Beta sandwich / IgG fold / Chromophore / ligand
Function / homology
Function and homology information


defense response to bacterium / DNA binding
Similarity search - Function
Neocarzinostatin-like / Neocarzinostatin family / Neocarzinostatin family / Neocarzinostatin-like / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-NCZ / Neocarzinostatin
Similarity search - Component
Biological speciesStreptomyces carzinostaticus (bacteria)
MethodSOLUTION NMR / Simulated annealing with torsion angle dynamics
AuthorsUrbaniak, M.D. / Muskett, F.W. / Finucane, M.D. / Caddick, S. / Woolfson, D.N.
CitationJournal: Biochemistry / Year: 2002
Title: Solution Structure of a Novel Chromoprotein Derived from Apo-Neocarzinostatin and a Synthetic Chromophore
Authors: Urbaniak, M.D. / Muskett, F.W. / Finucane, M.D. / Caddick, S. / Woolfson, D.N.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (Apo-Neocarzinostatin)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5582
Polymers12,2271
Non-polymers3301
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)44 / 100structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PROTEIN (Apo-Neocarzinostatin) / NCS / MITOMALCIN / MMC


Mass: 12227.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces carzinostaticus (bacteria)
Plasmid: pCANTABB5 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3R9
#2: Chemical ChemComp-NCZ / 2-HYDROXY-7-METHOXY-5-METHYL-NAPHTHALENE-1-CARBOXYLIC ACID MESO-2,5-DIHYDROXY-CYCLOPENT-3-ENYL ESTER


Mass: 330.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O6
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-1H-15N TOCSY
1213D 1H-1H-15N NOESY
1313D HNHA
1413D HNHB
1512D 1H-15N HSQC
1612D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.0 mM u-15N 1, 1.0 mM 2, 25 mM phosphate pH 5.0, 0.1 mM TSP, 0.005% sodium azide w/v
Solvent system: 80% H2O 10% D2O 10% d4-MeOH
Sample conditionsIonic strength: 25 mM sodium phosphate / pH: 5 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipesgi6xDelaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A.processing
XEASY1.3.13Bartels, C., Xia, T. H., Billeter, M., Guntert, P., and Wurthrich, K.analysis
DYANAGuntert, Mumenthaler, Wurthrichrefinement
RefinementMethod: Simulated annealing with torsion angle dynamics / Software ordinal: 1
Details: RESTRAINTS FOR STRUCTURE CALCULATION: INTERMOLECULAR NOES 20, INTRARESIDUE NOES 173, SEQUENTIAL NOES (I, I + 1) 227, MEDIUM-RANGE NOES (I, I+2 - I+4) 115, LONG-RANGE NOES (I, I>5) 295, PSI ...Details: RESTRAINTS FOR STRUCTURE CALCULATION: INTERMOLECULAR NOES 20, INTRARESIDUE NOES 173, SEQUENTIAL NOES (I, I + 1) 227, MEDIUM-RANGE NOES (I, I+2 - I+4) 115, LONG-RANGE NOES (I, I>5) 295, PSI ANGLE RESTRAINTS 39, HYDROGEN BONDS 74, DISULPHIDE BONDS 12.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 44

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