HEADER HYDROLASE 15-JUN-03 1UG8 TITLE NMR STRUCTURE OF THE R3H DOMAIN FROM POLY(A)-SPECIFIC RIBONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY(A)-SPECIFIC RIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: R3H DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RIKEN CDNA 1200003I18; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P020513-14; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS R3H DOMAIN, POLY(A)-SPECIFIC 3'-EXORIBONUCLEASE, PARN, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL KEYWDS 3 GENOMICS, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.NAGATA,Y.MUTO,N.HAYAMI,H.UDA,M.SHIROUZU,T.TERADA,T.KIGAWA,M.INOUE, AUTHOR 2 T.YABUKI,M.AOKI,E.SEKI,T.MATSUDA,H.HIROTA,M.YOSHIDA,N.KOBAYASHI, AUTHOR 3 A.TANAKA,T.OSANAI,Y.MATSUO,T.ARAKAWA,P.CARNINCI,J.KAWAI, AUTHOR 4 Y.HAYASHIZAKI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 5 INITIATIVE (RSGI) REVDAT 4 27-DEC-23 1UG8 1 REMARK REVDAT 3 02-MAR-22 1UG8 1 REMARK SEQADV REVDAT 2 24-FEB-09 1UG8 1 VERSN REVDAT 1 17-AUG-04 1UG8 0 JRNL AUTH T.NAGATA,Y.MUTO,N.HAYAMI,H.UDA,M.SHIROUZU,T.TERADA,T.KIGAWA, JRNL AUTH 2 M.INOUE,T.YABUKI,M.AOKI,E.SEKI,T.MATSUDA,H.HIROTA,M.YOSHIDA, JRNL AUTH 3 N.KOBAYASHI,A.TANAKA,T.OSANAI,Y.MATSUO,T.ARAKAWA,P.CARNINCI, JRNL AUTH 4 J.KAWAI,Y.HAYASHIZAKI,S.YOKOYAMA JRNL TITL NMR STRUCTURE OF THE R3H DOMAIN FROM POLY(A)-SPECIFIC JRNL TITL 2 RIBONUCLEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRVIEW 5.0.4, CYANA 1.0 REMARK 3 AUTHORS : JOHNSON (NMRVIEW), GUENTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UG8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000005795. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 100MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.45MM PROTEIN U-15N, 13C; 50MM REMARK 210 PHOSPHATE BUFFER NA; 100MM REMARK 210 NA2SO4; 1MM DTT; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY 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 : CYANA 1.0, NMRPIPE 1.8, KUJIRA REMARK 210 0.816 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 THR A 48 H LYS A 52 1.49 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 SER A 2 83.66 55.90 REMARK 500 1 SER A 3 -53.53 -164.11 REMARK 500 1 TYR A 53 79.42 -152.69 REMARK 500 1 THR A 64 -148.40 -124.65 REMARK 500 1 ASP A 65 -62.02 -90.07 REMARK 500 1 GLU A 68 -168.49 45.21 REMARK 500 2 THR A 64 -146.09 -120.22 REMARK 500 2 ASP A 65 -63.07 -92.54 REMARK 500 2 GLU A 68 174.80 65.50 REMARK 500 2 ARG A 69 97.68 -50.85 REMARK 500 3 SER A 2 92.79 44.68 REMARK 500 3 SER A 3 79.82 -104.33 REMARK 500 3 GLU A 27 -63.64 -92.28 REMARK 500 3 TYR A 53 83.21 -160.22 REMARK 500 3 THR A 64 -147.32 -122.41 REMARK 500 3 ASP A 65 -62.62 -92.53 REMARK 500 3 GLU A 68 173.48 64.41 REMARK 500 3 ARG A 69 101.30 -46.46 REMARK 500 4 GLU A 27 -66.67 -92.18 REMARK 500 4 TYR A 53 80.80 -155.05 REMARK 500 4 LYS A 67 -63.59 -101.25 REMARK 500 4 GLU A 68 93.86 87.03 REMARK 500 4 ARG A 69 82.25 52.62 REMARK 500 5 SER A 2 91.69 42.61 REMARK 500 5 SER A 3 -53.73 -140.62 REMARK 500 5 CYS A 37 -179.05 -65.52 REMARK 500 5 TYR A 53 81.01 -154.91 REMARK 500 5 THR A 64 -141.67 -129.54 REMARK 500 5 ASP A 65 -63.38 -92.75 REMARK 500 5 GLU A 68 -179.67 56.28 REMARK 500 5 ARG A 69 93.08 -47.07 REMARK 500 6 SER A 2 91.59 50.51 REMARK 500 6 TYR A 53 81.23 -155.56 REMARK 500 6 THR A 64 -148.09 -110.28 REMARK 500 6 ASP A 65 -64.58 -92.72 REMARK 500 6 GLU A 68 -164.25 53.62 REMARK 500 6 GLU A 79 -70.45 -66.78 REMARK 500 7 SER A 2 -58.83 -142.83 REMARK 500 7 SER A 3 -63.17 -124.99 REMARK 500 7 TYR A 53 79.85 -151.96 REMARK 500 7 THR A 64 -147.64 -129.00 REMARK 500 7 ASP A 65 -63.17 -92.81 REMARK 500 7 GLU A 68 -174.17 71.44 REMARK 500 7 ARG A 69 92.25 -49.58 REMARK 500 8 TYR A 53 80.24 -152.75 REMARK 500 8 THR A 64 -149.40 -120.80 REMARK 500 8 ASP A 65 -63.19 -92.75 REMARK 500 8 GLU A 68 168.67 68.15 REMARK 500 8 ARG A 69 108.60 -45.28 REMARK 500 9 THR A 48 -70.31 -56.75 REMARK 500 REMARK 500 THIS ENTRY HAS 128 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MMK001005079.1 RELATED DB: TARGETDB DBREF 1UG8 A 8 81 UNP Q8VDG3 PARN_MOUSE 169 242 SEQADV 1UG8 GLY A 1 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 SER A 2 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 SER A 3 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 GLY A 4 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 SER A 5 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 SER A 6 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 GLY A 7 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 SER A 82 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 GLY A 83 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 PRO A 84 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 SER A 85 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 SER A 86 UNP Q8VDG3 CLONING ARTIFACT SEQADV 1UG8 GLY A 87 UNP Q8VDG3 CLONING ARTIFACT SEQRES 1 A 87 GLY SER SER GLY SER SER GLY ASP GLN LYS LYS PHE ILE SEQRES 2 A 87 ASP GLN VAL ILE GLU LYS ILE GLU ASP PHE LEU GLN SER SEQRES 3 A 87 GLU GLU LYS ARG SER LEU GLU LEU ASP PRO CYS THR GLY SEQRES 4 A 87 PHE GLN ARG LYS LEU ILE TYR GLN THR LEU SER TRP LYS SEQRES 5 A 87 TYR PRO LYS GLY ILE HIS VAL GLU THR LEU GLU THR ASP SEQRES 6 A 87 LYS LYS GLU ARG HIS ILE VAL ILE SER LYS VAL ASP GLU SEQRES 7 A 87 GLU GLU ARG SER GLY PRO SER SER GLY HELIX 1 1 SER A 3 SER A 26 1 24 HELIX 2 2 GLY A 39 TYR A 53 1 15 SHEET 1 A 3 SER A 31 GLU A 33 0 SHEET 2 A 3 HIS A 70 LYS A 75 -1 O ILE A 73 N LEU A 32 SHEET 3 A 3 ILE A 57 LEU A 62 -1 N LEU A 62 O HIS A 70 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 MODEL 1