PDB Short entry for 1V80 HEADER SIGNALING PROTEIN 27-DEC-03 1V80 TITLE SOLUTION STRUCTURES OF UBIQUITIN AT 30 BAR AND 3 KBAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN/60S RIBOSOMAL PROTEIN L40 FUSION; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS PRESSURE, SIGNALING PROTEIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.KITAHARA,S.YOKOYAMA,K.AKASAKA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 6 27-DEC-23 1V80 1 REMARK REVDAT 5 02-MAR-22 1V80 1 REMARK REVDAT 4 24-FEB-09 1V80 1 VERSN REVDAT 3 16-OCT-07 1V80 1 AUTHOR KEYWDS REMARK REVDAT 2 08-MAR-05 1V80 1 JRNL REVDAT 1 15-FEB-05 1V80 0 JRNL AUTH R.KITAHARA,S.YOKOYAMA,K.AKASAKA JRNL TITL NMR SNAPSHOTS OF A FLUCTUATING PROTEIN STRUCTURE: UBIQUITIN JRNL TITL 2 AT 30 BAR-3 KBAR. JRNL REF J.MOL.BIOL. V. 347 277 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15740740 JRNL DOI 10.1016/J.JMB.2005.01.052 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.0, CYANA 1.06 REMARK 3 AUTHORS : UNKNOWN (XWINNMR), GUNTERT. P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1269 RESTRAINTS, 1185 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 84 REMARK 3 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1V80 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000006321. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 293 REMARK 210 PH : 4.6; 4.6 REMARK 210 IONIC STRENGTH : 0.03; 0.03 REMARK 210 PRESSURE : 30 BAR; 1 BAR REMARK 210 SAMPLE CONTENTS : 10MM UBIQUITIN; 30MM DEUTRATED REMARK 210 ACETATE BUFFER; 92% H2O, 8% D2O; REMARK 210 3.0MM 15N-UBIQUITIN; 30MM REMARK 210 DEUTRATED ACETATE BUFFER; 95% REMARK 210 H2O, 5% D20; 1.8MM 15N-13C- REMARK 210 UBIQUITIN; 30MM DEUTRATED REMARK 210 ACETATE BUFFER; 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HNCA-J; 2D-HNCA REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.2, CYANA 1.06, NMRVIEW REMARK 210 5.0.4 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS A 6 H LEU A 69 1.50 REMARK 500 H PHE A 4 O SER A 65 1.54 REMARK 500 O ILE A 3 H LEU A 15 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LYS A 11 136.29 -37.18 REMARK 500 1 ARG A 42 101.79 -160.23 REMARK 500 1 GLN A 62 -158.81 -130.24 REMARK 500 1 LEU A 73 170.04 -59.52 REMARK 500 1 ARG A 74 -174.09 -63.76 REMARK 500 2 THR A 7 -154.85 -80.07 REMARK 500 2 ASP A 21 -175.54 -64.56 REMARK 500 2 ARG A 42 96.32 -160.21 REMARK 500 2 LYS A 63 140.75 -39.88 REMARK 500 2 GLU A 64 36.99 76.40 REMARK 500 2 LEU A 73 -151.39 36.69 REMARK 500 3 GLU A 16 62.04 -114.75 REMARK 500 3 ASP A 21 -166.74 -65.28 REMARK 500 3 LYS A 33 -70.60 -35.68 REMARK 500 3 ARG A 42 103.79 -160.06 REMARK 500 3 GLN A 62 -157.84 -133.17 REMARK 500 3 LEU A 73 170.58 -55.64 REMARK 500 3 ARG A 74 176.67 64.74 REMARK 500 4 GLU A 16 74.48 -107.51 REMARK 500 4 ASP A 21 -169.06 -74.09 REMARK 500 4 LYS A 33 -71.08 -42.87 REMARK 500 4 ARG A 42 102.60 -160.47 REMARK 500 4 ASN A 60 4.12 80.34 REMARK 500 4 LEU A 73 176.70 -56.98 REMARK 500 4 ARG A 74 84.77 25.20 REMARK 500 5 ASP A 21 -173.52 -63.10 REMARK 500 5 GLN A 62 -152.96 -129.33 REMARK 500 5 LEU A 73 -174.43 -67.81 REMARK 500 6 GLU A 16 77.36 -113.12 REMARK 500 6 ASP A 21 176.24 -54.35 REMARK 500 6 ARG A 42 100.14 -160.41 REMARK 500 6 LYS A 63 146.22 -39.10 REMARK 500 6 LEU A 73 178.89 -59.13 REMARK 500 6 ARG A 74 137.71 -38.04 REMARK 500 7 LYS A 11 137.96 -39.66 REMARK 500 7 ASP A 21 -172.36 -65.96 REMARK 500 7 ARG A 42 105.62 -160.30 REMARK 500 7 LEU A 73 -158.55 39.59 REMARK 500 8 LYS A 11 128.83 -35.23 REMARK 500 8 ARG A 42 103.03 -160.32 REMARK 500 8 ALA A 46 47.55 39.61 REMARK 500 8 ASN A 60 -0.19 80.02 REMARK 500 8 GLU A 64 43.95 70.84 REMARK 500 8 LEU A 73 -179.26 -57.88 REMARK 500 8 ARG A 74 138.15 -37.89 REMARK 500 9 LYS A 11 119.81 -36.77 REMARK 500 9 GLU A 16 69.02 -107.81 REMARK 500 9 ALA A 46 52.64 38.78 REMARK 500 9 GLN A 62 -158.22 -143.83 REMARK 500 9 GLU A 64 38.61 73.32 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1V81 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT 3 KBAR REMARK 900 RELATED ID: MY_001000119.1 RELATED DB: TARGETDB DBREF 1V80 A 1 76 UNP P62990 UBIQ_BOVIN 1 76 SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 GLN A 41 5 5 SHEET 1 A 4 THR A 12 LEU A 15 0 SHEET 2 A 4 ILE A 3 LYS A 6 -1 N ILE A 3 O LEU A 15 SHEET 3 A 4 THR A 66 VAL A 70 1 O LEU A 69 N LYS A 6 SHEET 4 A 4 ARG A 42 ILE A 44 -1 N ILE A 44 O HIS A 68 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000