HEADER VIRAL PROTEIN 15-JUL-20 7CK5 TITLE SOLUTION STRUCTURE OF 28 AMINO ACID POLYPEPTIDE (354-381) IN PLANTAGO TITLE 2 ASIATICA MOSAIC VIRUS REPLICASE BOUND TO SDS MICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLAMV REPLICASE PEPTIDE FROM RNA-DEPENDENT RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLANTAGO ASIATICA MOSAIC POTEXVIRUS; SOURCE 3 ORGANISM_COMMON: P1AMV; SOURCE 4 ORGANISM_TAXID: 28354; SOURCE 5 GENE: RDRP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 OTHER_DETAILS: CELL FREE EXPRESSION SYSTEM KEYWDS REPLICASE, METHYLTRANSFERASE, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.KOMATSU,N.SASAKI,T.YOSHIDA,K.SUZUKI,Y.MASUJIMA,M.HASHIMOTO, AUTHOR 2 S.WATANABE,N.TOCHIO,T.KIGAWA,Y.YAMAJI,K.OSHIMA,S.NAMBA,R.NELSON, AUTHOR 3 T.ARIE REVDAT 4 15-MAY-24 7CK5 1 REMARK REVDAT 3 14-JUN-23 7CK5 1 REMARK REVDAT 2 02-FEB-22 7CK5 1 JRNL REVDAT 1 21-JUL-21 7CK5 0 JRNL AUTH K.KOMATSU,N.SASAKI,T.YOSHIDA,K.SUZUKI,Y.MASUJIMA, JRNL AUTH 2 M.HASHIMOTO,S.WATANABE,N.TOCHIO,T.KIGAWA,Y.YAMAJI,K.OSHIMA, JRNL AUTH 3 S.NAMBA,R.S.NELSON,T.ARIE JRNL TITL IDENTIFICATION OF A PROLINE-KINKED AMPHIPATHIC ALPHA-HELIX JRNL TITL 2 DOWNSTREAM FROM THE METHYLTRANSFERASE DOMAIN OF A POTEXVIRUS JRNL TITL 3 REPLICASE AND ITS ROLE IN VIRUS REPLICATION AND PERINUCLEAR JRNL TITL 4 COMPLEX FORMATION. JRNL REF J.VIROL. V. 95 90620 2021 JRNL REFN ESSN 1098-5514 JRNL PMID 34346768 JRNL DOI 10.1128/JVI.01906-20 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017709. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] PLAMV REMARK 210 REPLICASE PEPTIDE, 20 MM [U-2H] REMARK 210 SODIUM ACETATE, 100 MM [U-2H] REMARK 210 SDS, 10 % [U-2H] D2O, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, NMRVIEW, MAGRO REMARK 210 -NMRVIEW, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 12 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 14 ARG A 12 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 15 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 ARG A 12 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES 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 3 GLU A 2 150.56 63.54 REMARK 500 4 GLU A 2 -21.81 -153.92 REMARK 500 5 GLU A 2 49.05 -79.26 REMARK 500 10 GLU A 2 48.81 -79.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 14 ARG A 12 0.09 SIDE CHAIN REMARK 500 19 ARG A 12 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36361 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF 28 AMINO ACID POLYPEPTIDE (354-381) IN REMARK 900 PLANTAGO ASIATICA MOSAIC VIRUS REPLICASE BOUND TO SDS MICELLE DBREF 7CK5 A 1 28 UNP B1B578 B1B578_P1AMV 354 381 SEQRES 1 A 28 PHE GLU ASP ILE LEU SER GLY ASN LEU LEU GLN ARG MET SEQRES 2 A 28 LEU ARG PRO LEU ARG SER GLY LEU THR GLN LEU LEU ASP SEQRES 3 A 28 PHE PHE HELIX 1 AA1 ASP A 3 SER A 6 5 4 HELIX 2 AA2 GLY A 7 LEU A 14 1 8 HELIX 3 AA3 LEU A 17 ASP A 26 1 10 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 TER 475 PHE A 28 ENDMDL MODEL 2 TER 475 PHE A 28 ENDMDL MODEL 3 TER 475 PHE A 28 ENDMDL MODEL 4 TER 475 PHE A 28 ENDMDL MODEL 5 TER 475 PHE A 28 ENDMDL MODEL 6 TER 475 PHE A 28 ENDMDL MODEL 7 TER 475 PHE A 28 ENDMDL MODEL 8 TER 475 PHE A 28 ENDMDL MODEL 9 TER 475 PHE A 28 ENDMDL MODEL 10 TER 475 PHE A 28 ENDMDL MODEL 11 TER 475 PHE A 28 ENDMDL MODEL 12 TER 475 PHE A 28 ENDMDL MODEL 13 TER 475 PHE A 28 ENDMDL MODEL 14 TER 475 PHE A 28 ENDMDL MODEL 15 TER 475 PHE A 28 ENDMDL MODEL 16 TER 475 PHE A 28 ENDMDL MODEL 17 TER 475 PHE A 28 ENDMDL MODEL 18 TER 475 PHE A 28 ENDMDL MODEL 19 TER 475 PHE A 28 ENDMDL MODEL 20 TER 475 PHE A 28 ENDMDL MASTER 142 0 0 3 0 0 0 6 232 1 0 3 END