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- PDB-2lgo: Solution NMR structure of a FKBP-type peptidyl-prolyl cis-trans i... -

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Basic information

Entry
Database: PDB / ID: 2lgo
TitleSolution NMR structure of a FKBP-type peptidyl-prolyl cis-trans isomerase from Giardia lamblia, Seattle Structural Genomics Center for Infectious Disease target GilaA.00840.a
ComponentsFKBP
KeywordsISOMERASE / infectious disease / giardiasis / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
peptidylprolyl isomerase
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: Solution structure of a putative FKBP-type peptidyl-propyl cis-trans isomerase from Giardia lamblia.
Authors: Buchko, G.W. / Hewitt, S.N. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJul 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jun 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 1.3May 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: FKBP


Theoretical massNumber of molelcules
Total (without water)14,1601
Polymers14,1601
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 FKBP / FKBP-type peptidyl-prolyl cis-trans isomerase


Mass: 14160.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_10450 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8I6M8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D HNCO
1713D HN(CA)CB
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
1112deuterium exchange
11213D C(CO)NH
11312D HBCBCGCDCDHD
11412D (HB)CB(CGCDCE)HE

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Sample preparation

Details
Solution-IDContentsSolvent system
11 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 mM [U-99% 13C; 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 mMentity-1[U-99% 13C; U-99% 15N]1
100 mMsodium chloride-21
20 mMTRIS-31
1 mMDTT-41
1 mMentity-5[U-99% 13C; 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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
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 0% 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 constraintsHydrogen bond constraints total count: 76 / Protein phi angle constraints total count: 75 / Protein psi angle constraints total count: 75
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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