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- PDB-5vto: Solution Structure of BlsM -

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Basic information

Entry
Database: PDB / ID: 5vto
TitleSolution Structure of BlsM
ComponentsBlasticidin M
KeywordsHYDROLASE / cytosine / Deaminase / biosynthesis
Function / homologyRossmann fold - #450 / transferase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein / Putative (Deoxy)cytidine deoxyribosyltransferase
Function and homology information
Biological speciesStreptomyces griseochromogenes (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKang, M. / Doddapaneni, K. / Heppner, Z. / Wu, Z.
CitationJournal: To Be Published
Title: Solution Structure of the NUCLEOTIDE hydrolase BlsM: Implication of its Substrate Specificity
Authors: Kang, M. / Doddapaneni, K. / Heppner, Z. / Wu, Z.
History
DepositionMay 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Blasticidin M
B: Blasticidin M


Theoretical massNumber of molelcules
Total (without water)35,7152
Polymers35,7152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Homodimer, mass spectrometry, Homodimer
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Blasticidin M


Mass: 17857.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseochromogenes (bacteria)
Gene: AVL59_19940 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1BCS8, UniProt: Q841K1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic13D HNCA
123isotropic13D HN(CA)CB
133isotropic13D HNCO
143isotropic13D HN(CO)CA
153isotropic13D HN(COCA)CB
162isotropic13D (H)CCH-TOCSY
174isotropic12D 1H-13C HSQC
181isotropic13D 15N NOESY-TROSY
192isotropic13D HMQC-NOESY-HSQC
1105isotropic13D 15N/13C-filtered 13C-edited NOESY
1116isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution125 mM sodium phosphate, 2 mM DTT, 25 mM sodium chloride, 2 mM beta-mercaptoethanol, 0.02 % sodium azide, 0.8 mM [U-15N] Blasticidin M, 92% H2O/8% D2OU-15N Labeled BlsM15N92% H2O/8% D2O
solution20.02 % sodium azide, 0.8 mM [U-13C; U-15N] Blasticidin M, 92% H2O/8% D2OU-15N,13C Doubly Labeled BlsM15N/13C92% H2O/8% D2O
solution30.8 mM [U-100% 13C; U-100% 15N; U-95% 2H] Blasticidin M, 92% H2O/8% D2OU-2H,15N,13C Triply Labeled BlsM2H/15N/13C92% H2O/8% D2O
solution40.8 mM [U-10% 13C; U-100% 15N] Blasticidin M, 92% H2O/8% D2OU-15N and 10% 13C Labeled BlsM10%13C92% H2O/8% D2O
solution51.25 mM [U-15N] Blasticidin M, 1.25 mM [U-13C; U-15N] Blasticidin M, 92% H2O/8% D2Oequimolar mixture of U-15N and U-15N,13C Doubly Labeled BlsM1:1 Mix92% H2O/8% D2O
solution60.8 mM [U-15N] Blasticidin M, 92% H2O/8% D2OAlligned92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphatenatural abundance1
2 mMDTTnatural abundance1
25 mMsodium chloridenatural abundance1
2 mMbeta-mercaptoethanolnatural abundance1
0.02 %sodium azidenatural abundance1
0.8 mMBlasticidin M[U-15N]1
0.02 %sodium azidenatural abundance2
0.8 mMBlasticidin M[U-13C; U-15N]2
0.8 mMBlasticidin M[U-100% 13C; U-100% 15N; U-95% 2H]3
0.8 mMBlasticidin M[U-10% 13C; U-100% 15N]4
1.25 mMBlasticidin M[U-15N]5
1.25 mMBlasticidin M[U-13C; U-15N]6
0.8 mMBlasticidin M[U-15N]7
Sample conditionsIonic strength: 178 mM / Ionic strength err: 1 / Label: Condition_1 / pH: 6.50 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 308 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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