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- PDB-2lzu: Solution structure of LIMD2 -

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Basic information

Entry
Database: PDB / ID: 2lzu
TitleSolution structure of LIMD2
ComponentsLIM domain-containing protein 2
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsTalebzadeh Farooji, M. / Peng, H. / Rauscher, F.J. / Borden, K.K.L. / Osborne, M.J.
CitationJournal: To be Published
Title: Solution Structure of LIMD2
Authors: Talebzadeh Farooji, M.
History
DepositionOct 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIM domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4493
Polymers8,3191
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 450structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein LIM domain-containing protein 2


Mass: 8318.658 Da / Num. of mol.: 1 / Fragment: LIM zinc-binding domain residues 33-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMD2, SB143 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BT23
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1222D 1H-15N HSQC
1312D 1H-13C HSQC
1432D DQF-COSY
1532D 1H-1H TOCSY
1632D 1H-1H NOESY
1743D (H)CCH-TOCSY
1823D 1H-15N NOESY
1943D 1H-13C NOESY
11013D H(CCO)NH
11113D CBCA(CO)NH
11213D HBHA(CO)NH
11323D HNHB

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Sample preparation

Details
Solution-IDContentsSolvent system
1300-500 uM [U-99% 13C; U-99% 15N] LIMD2, 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
2300-500 uM [U-99% 15N] LIMD2, 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
3300-500 uM LIMD2, 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 100% D2O100% D2O
4300-500 uM [U-99% 13C; U-99% 15N] LIMD2, 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMLIMD2-1[U-99% 13C; U-99% 15N]300-5001
50 mMsodium phosphate-21
100 mMsodium chloride-31
1 mMTCEP-41
uMLIMD2-5[U-99% 15N]300-5002
50 mMsodium phosphate-62
100 mMsodium chloride-72
1 mMTCEP-82
uMLIMD2-9300-5003
50 mMsodium phosphate-103
100 mMsodium chloride-113
1 mMTCEP-123
uMLIMD2-13[U-99% 13C; U-99% 15N]300-5004
50 mMsodium phosphate-144
100 mMsodium chloride-154
1 mMTCEP-164
Sample conditionsIonic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 25 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesautomated chemical shift asignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichvisualization
PyMOLWarren Delanovisualization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 450 / Conformers submitted total number: 10

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