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- PDB-2lht: Solution structure of Venturia inaequalis cellophane-induced 1 pr... -

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Basic information

Entry
Database: PDB / ID: 2lht
TitleSolution structure of Venturia inaequalis cellophane-induced 1 protein (ViCin1) domains 1 and 2
ComponentsCellophane-induced protein 1
KeywordsCELL ADHESION / secreted repeat domain
Function / homologyDNA polymerase; domain 1 - #20 / Cellophane-induced protein 1 / : / : / Cellophane-induced 1 (cin1) repeat / DNA polymerase; domain 1 / Helix non-globular / Special / Cellophane-induced protein 1
Function and homology information
Biological speciesVenturia inaequalis (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMesarich, C.H. / Schmitz, M. / Tremouilhac, P. / Greenwood, D.R. / Mcgillivray, D.J. / Templeton, M.D. / Dingley, A.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Structure, dynamics and domain organization of the repeat protein Cin1 from the apple scab fungus.
Authors: Mesarich, C.H. / Schmitz, M. / Tremouilhac, P. / McGillivray, D.J. / Templeton, M.D. / Dingley, A.J.
History
DepositionAug 16, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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_nmr_spectrometer.model
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellophane-induced protein 1


Theoretical massNumber of molelcules
Total (without water)13,6491
Polymers13,6491
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 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cellophane-induced protein 1


Mass: 13649.398 Da / Num. of mol.: 1 / Fragment: UNP residues 26-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venturia inaequalis (fungus) / Strain: MNH135 / Gene: CIN1, ViCin1 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: A8W3P3
Has protein modificationY
Sequence detailsTHE AUTHOR STATES THAT THE ACCESSION CODE FOR THE PROTEIN SEQUENCE IS ABW70130.2. THE ADDITIONAL ...THE AUTHOR STATES THAT THE ACCESSION CODE FOR THE PROTEIN SEQUENCE IS ABW70130.2. THE ADDITIONAL GLU RESIDUE INSERTED AT POSITION 72 OF THE PROTEIN SEQUENCE IN VERSION ABW70130.1 HAS BEEN REMOVED IN VERSION ABW70130.2.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D CBCANH
1513D CBCA(CO)NH
1613D HNCO
1713D HCAN
1813D H(CCO)NH
1913D C(CO)NH
11013D 1H-15N TOCSY
11113D (H)CCH-TOCSY
11212D HBCBCGCDHG
11312D (HB)CB(CGCDCE)HE
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic
11613D 1H-13C NOESY aromatic
11712D 1H-15N IPAP-HSQC
11822D 1H-15N IPAP-HSQC
11912D 1H-15N R2 relaxation
12012D 1H-15N R1 relaxation
12112D 1H-15N heteronuclear NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-0.8 mM [U-99% 13C; U-99% 15N] ViCin1-D1D2, 25 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-99% 13C; U-99% 15N] ViCin1-D1D2, 25 mM potassium phosphate, 5-6 % polyacrylamide gel, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMViCin1-D1D2-1[U-99% 13C; U-99% 15N]0.6-0.81
25 mMpotassium phosphate-21
1.0 mMViCin1-D1D2-3[U-99% 13C; U-99% 15N]2
25 mMpotassium phosphate-42
%polyacrylamide gel-55-62
Sample conditionsIonic strength: 0.05 / pH: 6.2 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1pl3Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNMR2.07CCPNpeak picking
CcpNMR2.07CCPNchemical shift assignment
UNIO102Herrmannstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement against distance, torsion angle and RDC constraints in a 8 Angstrom water shell, using a modified version of the WaterRefCNS scripts. Disulfide bonds between residues 47-57, 64- ...Details: Refinement against distance, torsion angle and RDC constraints in a 8 Angstrom water shell, using a modified version of the WaterRefCNS scripts. Disulfide bonds between residues 47-57, 64-77, 103-113 and 120-129 were added as topology patches in CNS.
NMR constraintsNOE constraints total: 1414 / NOE intraresidue total count: 411 / NOE long range total count: 148 / NOE medium range total count: 395 / NOE sequential total count: 460 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 93
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 14.367 ° / Maximum upper distance constraint violation: 0.303 Å
NMR ensemble rmsDistance rms dev: 0.062594 Å / Distance rms dev error: 0.00871323 Å

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