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- PDB-2lpd: Solution structure of a MbtH-like protein from Burkholderia pseud... -

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Basic information

Entry
Database: PDB / ID: 2lpd
TitleSolution structure of a MbtH-like protein from Burkholderia pseudomallei, the etiological agent responsible for melioidosis, Seattle Structural Genomics Center for Infectious Disease target BupsA.13472.b
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / infectious disease / melioidosis / Seattle Structural Genomics Center for Infectious Disease / SSGCID / drug target
Function / homologyMbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / siderophore biosynthetic process / cytosol / MbtH-like protein / MbtH-like domain-containing protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Solution structure of a MbtH-like protein from Burkholderia pseudomallei, the etiological agent responsible for melioidosis
Authors: Buchko, G.W. / Hewitt, S.N. / Napuli, A.J. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionFeb 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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_software.name / _struct_ref_seq_dif.details
Revision 1.2May 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,8051
Polymers10,8051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein


Mass: 10804.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BPSL1726, BURPS1710b_2147 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q63U90, UniProt: Q3JSB1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D 1H-15N NOESY
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HNCO
1813D C(CO)NH
192deuterium exchange

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
21.0 mM [U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity-1[U-99% 13C; U-99% 15N]1
100 mMsodium chloride-21
20 mMTRIS-31
1 mMDTT-41
1.0 mMentity-5[U-99% 15N]2
100 mMsodium chloride-62
20 mMTRIS-72
1 mMDTT-82
Sample conditionsIonic strength: 0.12 / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian VNMRSVarianVNMRS7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Felix2007Accelrys Software Inc.processing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.115Goddardpeak picking
Sparky3.115Goddarddata analysis
PSVSBhattacharya and Montelionedata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 1% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS.
NMR constraintsNOE constraints total: 959 / NOE intraresidue total count: 266 / NOE long range total count: 252 / NOE medium range total count: 151 / NOE sequential total count: 298 / Hydrogen bond constraints total count: 28 / Protein phi angle constraints total count: 47 / Protein psi angle constraints total count: 47
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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