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- PDB-2lcq: Solution structure of the endonuclease Nob1 from P.horikoshii -

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Basic information

Entry
Database: PDB / ID: 2lcq
TitleSolution structure of the endonuclease Nob1 from P.horikoshii
ComponentsPutative toxin VapC6
KeywordsMETAL BINDING PROTEIN / PIN domain / ZN ribbon domain / ribosome biogenesis
Function / homology
Function and homology information


RNA nuclease activity / ribosome biogenesis / endonuclease activity / Hydrolases; Acting on ester bonds / rRNA binding / magnesium ion binding
Similarity search - Function
Ribonuclease, PIN domain / RNA-binding protein NOB1 / PIN domain of ribonuclease / VapC family / 5'-nuclease / Rubrerythrin, domain 2 - #10 / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / Rubrerythrin, domain 2 ...Ribonuclease, PIN domain / RNA-binding protein NOB1 / PIN domain of ribonuclease / VapC family / 5'-nuclease / Rubrerythrin, domain 2 - #10 / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / Rubrerythrin, domain 2 / Single Sheet / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease Nob1
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsfewest violations, model 1
AuthorsVeith, T. / Martin, R. / Wurm, J.P. / Weis, B. / Duchardt-Ferner, E. / Safferthal, C. / Hennig, R. / Mirus, O. / Bohnsack, M.T. / Woehnert, J. / Schleiff, E.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural and functional analysis of the archaeal endonuclease Nob1.
Authors: Veith, T. / Martin, R. / Wurm, J.P. / Weis, B.L. / Duchardt-Ferner, E. / Safferthal, C. / Hennig, R. / Mirus, O. / Bohnsack, M.T. / Wohnert, J. / Schleiff, E.
History
DepositionMay 5, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Putative toxin VapC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3982
Polymers18,3321
Non-polymers651
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 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Putative toxin VapC6


Mass: 18332.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: vapC6, PH0709 / Production host: Escherichia coli (E. coli) / References: UniProt: O58440
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
1123D HN(CA)CB
1223D HNCO
1323D HBHA(CO)NH
1413D HNHA
1513D 1H-15N NOESY
1623D CBCA(CO)NH
1723D 1H-13C NOESY aromatic
1822D 1H-13C HSQC aromatic
1922D 1H-15N HSQC
11022D 1H-13C HSQC aliphatic
11123D 1H-13C NOESY aliphatic
11222D 1H-15N HSQC
11323D HNCA
11422D 1H-15N HSQC
11523D (H)CCH-TOCSY
11623D (H)CCH-COSY
11723D H(CCO)NH
11822D 1H-15N HSQC
11922D 1H-15N HSQC
12032D 1H-15N HSQC
12132D long range HNCO
12242D 1H-15N HSQC
12343D long range HNCO
12443D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-15N] PhNob1, 50 mM potassium chloride, 50 mM BisTris, 90 % H2O, 10 % D2O, 0.4 mM ZN, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-13C; U-15N] PhNob1, 50 mM potassium chloride, 50 mM BisTris, 90 % H2O, 10 % D20, 0.4 mM ZN, 90% H2O/10% D2O90% H2O/10% D2O
3300 uM [U-13C; U-15N] ZN ribbon domain, 300 uM ZN, 50 mM potassium chloride, 50 mM BisTris, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
4400 uM [U-13C; U-15N; U-2H] PIN domain, 50 mM potassium chloride, 50 mM BisTris, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMPhNob1-1[U-15N]1
50 mMpotassium chloride-21
50 mMBisTris-31
90 %H2O-41
10 %D2O-51
0.4 mMZN-61
0.4 mMPhNob1-7[U-13C; U-15N]2
50 mMpotassium chloride-82
50 mMBisTris-92
90 %H2O-102
10 %D20-112
0.4 mMZN-122
300 uMZN ribbon domain-13[U-13C; U-15N]3
300 uMZN-143
50 mMpotassium chloride-153
50 mMBisTris-163
90 %H2O-173
10 %D2O-183
400 uMPIN domain-19[U-13C; U-15N; U-2H]4
50 mMpotassium chloride-204
50 mMBisTris-214
90 %H2O-224
10 %D2O-234
Sample conditionsIonic strength: 83 / pH: 6.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004
Bruker AvanceBrukerAVANCE9505

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Processing

NMR software
NameVersionDeveloperClassification
OPALpKoradi, Billeter, G ntertrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichchemical shift assignment
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxstructure solution
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CANDIDHerrmann, Guntert and Wuthrichstructure solution
ATNOSHerrmann, Guntert and Wuthrichrefinement
CANDIDHerrmann, Guntert and Wuthrichrefinement
TOPSPIN_2.1Bruker Biospinprocessing
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: 7 steps of ATNOS/CANDID for automated NOE assignment using CYANA 3.0 as molecular dynamcis algorithm
NMR constraintsNOE constraints total: 3542 / NOE intraresidue total count: 651 / NOE long range total count: 1321 / NOE medium range total count: 639 / NOE sequential total count: 931 / Hydrogen bond constraints total count: 160 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 114 / Protein psi angle constraints total count: 114
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.49 Å / Maximum torsion angle constraint violation: 6.22 ° / Maximum upper distance constraint violation: 0.53 Å
NMR ensemble rmsDistance rms dev: 0.013 Å / Distance rms dev error: 0.001 Å

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