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- PDB-2lvc: Solution NMR Structure of Ig like domain (805-892) of Obscurin-li... -

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Basic information

Entry
Database: PDB / ID: 2lvc
TitleSolution NMR Structure of Ig like domain (805-892) of Obscurin-like protein 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8578K
ComponentsObscurin-like protein 1
KeywordsSTRUCTURAL PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


3M complex / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / regulation of mitotic nuclear division / Golgi organization / intercalated disc / cytoskeleton organization ...3M complex / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / regulation of mitotic nuclear division / Golgi organization / intercalated disc / cytoskeleton organization / Z disc / microtubule cytoskeleton organization / Neddylation / centrosome / perinuclear region of cytoplasm / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Obscurin-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPulavarti, S. / Eletsky, A. / Sukumaran, D.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Pederson, K. ...Pulavarti, S. / Eletsky, A. / Sukumaran, D.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Pederson, K. / Prestegard, J. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Ig like domain (805-892) of Obscurin-like protein 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8578K (CASP Target)
Authors: Pulavarti, S. / Eletsky, A. / Sukumaran, D.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Pederson, K. / Prestegard, J. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 30, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 29, 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: Obscurin-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,2521
Polymers10,2521
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Obscurin-like protein 1


Mass: 10252.415 Da / Num. of mol.: 1 / Fragment: Ig-like 6 domain residues 805-892
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0657, OBSL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: O75147

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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 (CT-27 ms) HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HN(CA)CO
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1822D 1H-13C (CT-28 ms) HSQC
1912D 1H-13C (CT-56 ms) HSQC
11012D 1H-13C (CT-42 ms) HSQC
11113D C(CO)NH
11213D (H)CCH-TOCSY
11313D HBHA(CO)NH
11413D H(CCO)NH
11513D (H)CCH-COSY (Aliphatic)
11613D (H)CCH-COSY (Aromatic)
11732D 1H-15N HSQC J-mod
11842D 1H-15N HSQC J-mod
11922D 1H-15N HSQC J-mod

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-5% 13C; U-100% 15N] HR8578K.010, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-5% 13C; U-100% 15N] HR8578K.010, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 12.5 mg/mL PF1 Phage, 80% H2O/20% D2O80% H2O/20% D2O
40.6 mM [U-5% 13C; U-100% 15N] HR8578K.010, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 4 % PEG, 80% H2O/20% D2O80% H2O/20% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHR8578K.009-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 %Proteinase Inhibitors-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
1.0 mMHR8578K.010-10[U-5% 13C; U-100% 15N]2
0.02 %NaN3-112
10 mMDTT-122
5 mMCaCL2-132
100 mMNaCL-142
1 %Proteinase Inhibitors-152
20 mMMES pH 6.5-162
10 %D2O-172
50 uMDSS-182
0.6 mMHR8578K.010-19[U-5% 13C; U-100% 15N]3
0.02 %NaN3-203
10 mMDTT-213
5 mMCaCL2-223
100 mMNaCL-233
1 %Proteinase Inhibitors-243
20 mMMES pH 6.5-253
10 %D2O-263
50 uMDSS-273
12.5 mg/mLPF1 Phage-283
0.6 mMHR8578K.010-29[U-5% 13C; U-100% 15N]4
0.02 %NaN3-304
10 mMDTT-314
5 mMCaCL2-324
100 mMNaCL-334
1 %Proteinase Inhibitors-344
20 mMMES pH 6.5-354
10 %D2O-364
50 uMDSS-374
4 %PEG-384
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichdata analysis
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
CSIWishart, D.S. and B.D. Sykes.data analysis
VnmrJVariancollection
PROSAGuntertprocessing
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESZweckstetter, Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSENSUS PEAK ASSIGNMENTS GENERATED FROM ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSENSUS PEAK ASSIGNMENTS GENERATED FROM THESE PARALLEL RUNS WERE SELECTED AND USED FOR FURTHER REFINEMENT WITH CYANA, THE RDC CONSTRAINTS WERE ADDED AT LATER STAGES. A TOTAL OF 20 CONFORMERS OUT OF 100 CONFORMERS WITH THE LOWEST TARGET FUNCTION WERE SELECTED FOR REFINEMENT WITH CNS USING CNS WATER BATH REFINEMENT
NMR constraintsNOE constraints total: 1334 / NOE intraresidue total count: 197 / NOE long range total count: 565 / NOE medium range total count: 198 / NOE sequential total count: 374
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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