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- PDB-2lgd: The high resolution structure of ubiquitin like domain of UBLCP1 -

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Basic information

Entry
Database: PDB / ID: 2lgd
TitleThe high resolution structure of ubiquitin like domain of UBLCP1
ComponentsUbiquitin-like domain-containing CTD phosphatase 1
KeywordsHYDROLASE / UBIQUITIN LIKE DOMAIN / UBLCP1 / RNA POLYMERASE II
Function / homology
Function and homology information


regulation of proteasome assembly / proteasome regulatory particle binding / negative regulation of ATP-dependent activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / protein dephosphorylation / nucleolus / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIID / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / HAD superfamily / HAD-like superfamily / Ubiquitin-like (UB roll) / Ubiquitin family ...HAD-superfamily hydrolase, subfamily IIID / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / HAD superfamily / HAD-like superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like domain-containing CTD phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsLee, W. / Ko, S.
CitationJournal: To be Published
Title: The High Resolution Structure of Ubiquitin Like Dom Ublcp1
Authors: Lee, N. / Ko, S.
History
DepositionJul 25, 2011Deposition site: BMRB / Processing site: PDBJ
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: Ubiquitin-like domain-containing CTD phosphatase 1


Theoretical massNumber of molelcules
Total (without water)9,1421
Polymers9,1421
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 #1minimized average structure

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Components

#1: Protein Ubiquitin-like domain-containing CTD phosphatase 1


Mass: 9141.800 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 1-81)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBLCP1 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WVY7, protein-serine/threonine phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1233D CBCA(CO)NH
1333D HNCO
1433D HNCA
1533D HN(CA)CB
1633D HBHA(CO)NH
1723D (H)CCH-TOCSY
1813D 1 15N NOESY
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 15N] UBIQUITIN-LIKE DOMAIN-CONTAINING CTD PHOSPHATASE 1-1, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-95% 13C] UBIQUITIN-LIKE DOMAIN-CONTAINING CTD PHOSPHATASE 1-2, 100% D2O100% D2O
31.5 mM [U-95% 13C; U-95% 15N] UBIQUITIN-LIKE DOMAIN-CONTAINING CTD PHOSPHATASE 1-3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMUBIQUITIN-LIKE DOMAIN-CONTAINING CTD PHOSPHATASE 1-1[U-99% 15N]1
1.5 mMUBIQUITIN-LIKE DOMAIN-CONTAINING CTD PHOSPHATASE 1-2[U-95% 13C]2
1.5 mMUBIQUITIN-LIKE DOMAIN-CONTAINING CTD PHOSPHATASE 1-3[U-95% 13C; U-95% 15N]3
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER DRX / Manufacturer: Bruker / Model: DRX / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
MOLMOL_NMRDRAWKoradi, Billeter and Wuthrichdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PROCHECKNMRLaskowski and MacArthurrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
XwinNMRBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxstructure solution
CYANA2.2.5P.GUNTERT ET AL.refinement
CYANA2.2.5P.GUNTERT ET AL.structure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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