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- PDB-2l95: Solution Structure of Cytotoxic T-Lymphocyte Antigent-2(Ctla prot... -

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Basic information

Entry
Database: PDB / ID: 2l95
TitleSolution Structure of Cytotoxic T-Lymphocyte Antigent-2(Ctla protein), Crammer at pH 6.0
ComponentsCrammer
KeywordsHYDROLASE / CRAMMER / CYSTEINE PROTEINASE INHIBITOR / INTRINSIC DISORDER P CTLA-2-LIKE PROTEIN
Function / homology
Function and homology information


short-term memory / cysteine-type endopeptidase inhibitor activity / long-term memory / endomembrane system / lysosome
Similarity search - Function
Helix Hairpins - #2250 / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine peptidase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
Model detailslowest energy, model 1
AuthorsTseng, T.S. / Cheng, C.S. / Liu, Y.N. / Lyu, P.C.
CitationJournal: Biochem.J. / Year: 2012
Title: A molten globule-to-ordered structure transition of Drosophila melanogaster crammer is required for its ability to inhibit cathepsin.
Authors: Tseng, T.S. / Cheng, C.S. / Chen, D.J. / Shih, M.F. / Liu, Y.N. / Hsu, S.T. / Lyu, P.C.
History
DepositionJan 31, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq_dif.details
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crammer


Theoretical massNumber of molelcules
Total (without water)9,5961
Polymers9,5961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5710 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Crammer / LP06209p


Mass: 9595.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CER, CER-RA, DMEL_CG10460 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A1ZBK7, Hydrolases; Acting on peptide bonds (peptidases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D DQF-COSY
1332D 1H-1H COSY
1432D 1H-1H NOESY
1523D CBCA(CO)NH
1623D HNCO
1723D HNCA
1823D HN(CA)CB
1923D HBHA(CO)NH
11023D HN(CO)CA
11123D 1H-15N NOESY
11223D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-99% 15N] CRAMMER-1, 10 mM Citric-acid phosphate-2, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 13C; U-99% 15N] CRAMMER-3, 10 mM Citric-acid phosphate-4, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM CRAMMER-5, 10 mM Citric-acid phosphate-6, 10mM citric-acid phosphate10mM citric-acid phosphate
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMCRAMMER-1[U-99% 15N]1
10 mMCitric-acid phosphate-21
0.5 mMCRAMMER-3[U-99% 13C; U-99% 15N]2
10 mMCitric-acid phosphate-42
0.5 mMCRAMMER-53
10 mMCitric-acid phosphate-63
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENdata analysis
SparkyGoddardstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
SparkyGoddardpeak picking
PSVSBhattacharya and Montelionestructure solution
PSVSBhattacharya and Montelionedata analysis
MOLMOLKoradi, Billeter and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichcollection
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10 / Representative conformer: 1

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