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- PDB-1cz4: NMR STRUCTURE OF VAT-N: THE N-TERMINAL DOMAIN OF VAT (VCP-LIKE AT... -

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Basic information

Entry
Database: PDB / ID: 1cz4
TitleNMR STRUCTURE OF VAT-N: THE N-TERMINAL DOMAIN OF VAT (VCP-LIKE ATPASE OF THERMOPLASMA)
ComponentsVCP-LIKE ATPASE
KeywordsHYDROLASE / DOUBLE-PSI BETA-BARREL / BETA-CLAM / SUBSTRATE RECOGNITION DOMAIN
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoplasma acidophilum (acidophilic)
MethodSOLUTION NMR / simulated annealing
AuthorsColes, M. / Diercks, T. / Liermann, J. / Groeger, A. / Rockel, B. / Baumeister, W. / Koretke, K. / Lupas, A. / Peters, J. / Kessler, H.
CitationJournal: Curr.Biol. / Year: 1999
Title: The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element.
Authors: Coles, M. / Diercks, T. / Liermann, J. / Groger, A. / Rockel, B. / Baumeister, W. / Koretke, K.K. / Lupas, A. / Peters, J. / Kessler, H.
History
DepositionSep 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VCP-LIKE ATPASE


Theoretical massNumber of molelcules
Total (without water)20,6501
Polymers20,6501
Non-polymers00
Water0
1


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

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Components

#1: Protein VCP-LIKE ATPASE


Mass: 20649.816 Da / Num. of mol.: 1
Fragment: N-TERMINAL DOMAIN: M1 TO E183 FOLLOWED BY A DIGLYCINE SPACER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / References: UniProt: O05209

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D CNH-NOESY
1313D NCH-NOESY
1413D CCH-NOESY
1523D 15N-SEPARATED NOESY
1623D NNH-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. 3JHNHA COUPLING-CONSTANTS FROM AN HNHA SPECTRUM

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Sample preparation

Details
Solution-IDContents
11.4 MM VAT-NU-15N,13C; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O
21.2 MM VAT-N U-15N; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
180 mM 5.9 AMBIENT 320 K
280 mM 5.9 AMBIENT 320 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5BRUKERcollection
XwinNMR2.5BRUKERprocessing
AURELIA2.5.11BRUKERdata analysis
X-PLOR3.851BRUNGERstructure solution
X-PLOR3.851BRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURES BASED ON 1923 DISTANCE RESTRAINTS; 1817 NOE BASED RESTRAINTS, 196 DIHEDRAL ANGLE RESTRAINTS, 56 J-COUPLING RESTRAINTS, 106 DISTANCE RESTRAINTS FOR H-BONDS, 158 CA AND 148 CB ...Details: STRUCTURES BASED ON 1923 DISTANCE RESTRAINTS; 1817 NOE BASED RESTRAINTS, 196 DIHEDRAL ANGLE RESTRAINTS, 56 J-COUPLING RESTRAINTS, 106 DISTANCE RESTRAINTS FOR H-BONDS, 158 CA AND 148 CB CHEMICAL SHIFT RESTRAINTS. REFINED WITH A CONFORMATIONAL DATABASE POTENTIAL
NMR ensembleConformers submitted total number: 1

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