HEADER RNA BINDING PROTEIN/RNA 15-AUG-18 6EEN TITLE CRYSTAL STRUCTURE OF A DESIGNER PENTATRICO PEPTIDE RNA BINDING TITLE 2 PROTEIN, BOUND TO A COMPLEX RNA TARGET AND FEATURING AN INFINITE TITLE 3 SUPERHELIX AND MICROHETEROGENEITY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNER PENTATRICOPEPTIDE PROTEIN DPPR10; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DESIGNER PENTATRICOPEPTIDE PROTEIN DPPR10; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DESIGNER PENTATRICOPEPTIDE PROTEIN DPPR10; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DESIGNER PENTATRICOPEPTIDE PROTEIN DPPR10; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: RNA (5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'); COMPND 19 CHAIN: F; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'); COMPND 23 CHAIN: G; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'); COMPND 27 CHAIN: H; COMPND 28 ENGINEERED: YES; COMPND 29 MOL_ID: 8; COMPND 30 MOLECULE: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'); COMPND 31 CHAIN: I; COMPND 32 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_TAXID: 4577; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 8 ORGANISM_TAXID: 4577; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 13 ORGANISM_TAXID: 4577; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 18 ORGANISM_TAXID: 4577; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 MOL_ID: 5; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 24 ORGANISM_TAXID: 4577; SOURCE 25 MOL_ID: 6; SOURCE 26 SYNTHETIC: YES; SOURCE 27 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 28 ORGANISM_TAXID: 4577; SOURCE 29 MOL_ID: 7; SOURCE 30 SYNTHETIC: YES; SOURCE 31 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 32 ORGANISM_TAXID: 4577; SOURCE 33 MOL_ID: 8; SOURCE 34 SYNTHETIC: YES; SOURCE 35 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 36 ORGANISM_TAXID: 4577 KEYWDS COMPLEX, PPR, RNA, HELICAL DISORDER, RNA BINDING PROTEIN, RNA BINDING KEYWDS 2 PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.W.SCHMIDBERGER,C.S.BOND REVDAT 3 11-OCT-23 6EEN 1 REMARK REVDAT 2 01-JAN-20 6EEN 1 REMARK REVDAT 1 21-AUG-19 6EEN 0 JRNL AUTH J.W.SCHMIDBERGER,C.S.BOND JRNL TITL CRYSTAL STRUCTURE OF A DESIGNER PENTATRICO PEPTIDE RNA JRNL TITL 2 BINDING PROTEIN, BOUND TO A COMPLEX RNA TARGET AND FEATURING JRNL TITL 3 AN INFINITE SUPERHELIX AND MICROHETEROGENEITY. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 23919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1207 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9776 REMARK 3 NUCLEIC ACID ATOMS : 765 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 214 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.99000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : -0.53000 REMARK 3 B12 (A**2) : -1.12000 REMARK 3 B13 (A**2) : -1.42000 REMARK 3 B23 (A**2) : -0.17000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.342 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.477 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6EEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953737 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25127 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 44.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5I9F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MG ACETATE, 0.05 M MES PH 5.6, REMARK 280 20% MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 300 REMARK: THIS PROTEIN:RNA DIMER ASSEMBLY IS REPRESENTED AS AN REMARK 300 OCTAMERIC ASSEMBLY DUE TO STRUCTURAL DISORDER/MICROHETEROGENEITY REMARK 300 RESULTING IN THE STRUCTURE BEING REFINED AS 4 PROTEIN CHAINS REMARK 300 (PARTIALLY OCCUPIED) + 4 RNA CHAINS (PARTIALLY OCCUPIED) 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, F, G, H, I 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 400 REMARK 400 COMPOUND REMARK 400 THE STRUCTURE FEATURES AN INFINITE SUPERHELIX THAT HAS INHERENT REMARK 400 HELICAL DISORDER. THIS MEANS WE DON'T KNOW WHERE IT BEGINS AND REMARK 400 ENDS. THIS LEADS TO MAP AVERAGING AT EACH POSITION IN THE REPEATING REMARK 400 HELIX. THE HIGHLY REDUNDANT DESIGN OF THE PROTEIN MEANS THIS REMARK 400 AVERAGING IS NOT AN ISSUES EXCEPT AT POSITIONS 5 AND 35 OF EACH REMARK 400 REPEAT THAT CHANGE TO BIND DIFFERENT BASES IN THE TARGET RNA. ALSO, REMARK 400 THE TARGET RNA WILL AVERAGE OUT. THE SOLUTION TO THIS WAS TO BUILD REMARK 400 THE STRUCTURE AS FOUR SUPERPOSED CHAINS FOR THE PROTEIN AND FOUR REMARK 400 SUPERPOSED CHAINS FOR THE RNA. EACH CASE ADDING UP TO AN OCCUPANCY REMARK 400 OF 1. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 LYS C 107 CG CD CE NZ REMARK 470 LYS D 107 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 PRO D 283 O HOH D 401 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 313 CD GLU A 313 OE2 0.074 REMARK 500 ASP B 74 C ASP B 74 O -0.118 REMARK 500 GLU B 313 CD GLU B 313 OE2 0.074 REMARK 500 GLU C 313 CD GLU C 313 OE2 0.073 REMARK 500 GLU D 313 CD GLU D 313 OE2 0.073 REMARK 500 U G 4 O3' U G 5 P 0.076 REMARK 500 U G 5 P U G 5 OP2 -0.114 REMARK 500 REMARK 500 REMARK: NULL 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 U G 6 C5' - C4' - O4' ANGL. DEV. = 5.5 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 ARG A 55 56.63 -117.21 REMARK 500 ARG A 90 64.73 -112.12 REMARK 500 PRO A 108 152.89 -45.59 REMARK 500 ARG A 125 60.05 -101.04 REMARK 500 ASP A 144 -168.54 -108.93 REMARK 500 ARG A 160 55.45 -106.28 REMARK 500 ARG A 195 58.26 -111.99 REMARK 500 ARG A 230 57.78 -104.44 REMARK 500 ARG A 265 60.32 -110.09 REMARK 500 ARG A 300 61.44 -102.85 REMARK 500 ARG B 55 56.39 -117.22 REMARK 500 ARG B 90 64.73 -112.17 REMARK 500 ARG B 125 60.10 -101.16 REMARK 500 ARG B 160 55.30 -106.17 REMARK 500 ASP B 179 -166.68 -121.16 REMARK 500 ARG B 195 58.23 -111.97 REMARK 500 ARG B 230 57.83 -104.45 REMARK 500 ASP B 249 -168.89 -116.14 REMARK 500 ARG B 265 60.19 -110.32 REMARK 500 ARG B 300 61.47 -103.95 REMARK 500 ARG C 55 56.39 -117.22 REMARK 500 ARG C 90 64.75 -112.11 REMARK 500 ARG C 125 59.91 -100.66 REMARK 500 ARG C 160 55.33 -106.19 REMARK 500 ARG C 195 58.23 -111.97 REMARK 500 ARG C 230 57.32 -104.32 REMARK 500 ARG C 265 60.11 -110.28 REMARK 500 ARG C 300 61.39 -103.98 REMARK 500 ARG D 55 56.43 -117.21 REMARK 500 ARG D 90 64.73 -112.12 REMARK 500 ARG D 125 60.07 -100.97 REMARK 500 ARG D 160 55.37 -106.37 REMARK 500 SER D 179 -166.94 -106.92 REMARK 500 ARG D 195 58.23 -111.97 REMARK 500 ARG D 230 57.83 -104.45 REMARK 500 ARG D 265 60.11 -110.13 REMARK 500 ARG D 300 61.41 -105.60 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 ARG C 125 0.23 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN IS DESIGNED BASED ON A CONSENSUS SEQUENCE OF MANY PPR REMARK 999 PROTEINS. CHAINS A TO D ARE REPETITIONS OF THE SAME SINGLE CHAIN REMARK 999 WITH MICROHETEROGENEITY AT POSITIONS 5 AND 35. THE PROTEIN IS REMARK 999 OBSERVED TO BIND TO THE RNA TARGET. THE ACTUAL TARGET SEQUENCE IS REMARK 999 GUAUCCUUAACCAUUUC. BECAUSE OF INFINITE NATURE OF SUPERHELIX, IT WAS REMARK 999 BUILT AS SUPERPOSED POLY X CHAINS WITH OCCUPANCIES MATCHING THEIR REMARK 999 FREQUENCY IN THE ACTUAL SEQUENCE MENTIONED ABOVE. DBREF 6EEN A 5 319 PDB 6EEN 6EEN 5 319 DBREF 6EEN B 5 319 PDB 6EEN 6EEN 5 319 DBREF 6EEN C 5 319 PDB 6EEN 6EEN 5 319 DBREF 6EEN D 5 319 PDB 6EEN 6EEN 5 319 DBREF 6EEN F 1 9 PDB 6EEN 6EEN 1 9 DBREF 6EEN G 1 9 PDB 6EEN 6EEN 1 9 DBREF 6EEN H 1 9 PDB 6EEN 6EEN 1 9 DBREF 6EEN I 1 9 PDB 6EEN 6EEN 1 9 SEQRES 1 A 315 VAL VAL THR TYR THR THR LEU ILE ASP GLY LEU ALA LYS SEQRES 2 A 315 ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN GLU SEQRES 3 A 315 MET LYS GLU LYS GLY VAL LYS PRO ASP VAL VAL THR TYR SEQRES 4 A 315 THR THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU SEQRES 5 A 315 GLU GLU ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS SEQRES 6 A 315 GLY VAL LYS PRO ASP VAL VAL THR TYR THR THR LEU ILE SEQRES 7 A 315 ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU SEQRES 8 A 315 GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS PRO SEQRES 9 A 315 ASP VAL VAL THR TYR THR THR LEU ILE ASP GLY LEU ALA SEQRES 10 A 315 LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN SEQRES 11 A 315 GLU MET LYS GLU LYS GLY VAL LYS PRO ASP VAL VAL THR SEQRES 12 A 315 TYR THR THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG SEQRES 13 A 315 LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS GLU SEQRES 14 A 315 LYS GLY VAL LYS PRO ASP VAL VAL THR TYR THR THR LEU SEQRES 15 A 315 ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA SEQRES 16 A 315 LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS SEQRES 17 A 315 PRO ASP VAL VAL THR TYR THR THR LEU ILE ASP GLY LEU SEQRES 18 A 315 ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE SEQRES 19 A 315 GLU GLU MET LYS GLU LYS GLY VAL LYS PRO ASP VAL VAL SEQRES 20 A 315 THR TYR THR THR LEU ILE ASP GLY LEU ALA LYS ALA GLY SEQRES 21 A 315 ARG LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS SEQRES 22 A 315 GLU LYS GLY VAL LYS PRO ASP VAL VAL THR TYR THR THR SEQRES 23 A 315 LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU SEQRES 24 A 315 ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL SEQRES 25 A 315 LYS PRO ASP SEQRES 1 B 315 VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU ALA LYS SEQRES 2 B 315 ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN GLU SEQRES 3 B 315 MET LYS GLU LYS GLY VAL LYS PRO ASP VAL VAL THR TYR SEQRES 4 B 315 ASN THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU SEQRES 5 B 315 GLU GLU ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS SEQRES 6 B 315 GLY VAL LYS PRO ASP VAL VAL THR TYR ASN THR LEU ILE SEQRES 7 B 315 ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU SEQRES 8 B 315 GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS PRO SEQRES 9 B 315 ASP VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU ALA SEQRES 10 B 315 LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN SEQRES 11 B 315 GLU MET LYS GLU LYS GLY VAL LYS PRO ASP VAL VAL THR SEQRES 12 B 315 TYR ASN THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG SEQRES 13 B 315 LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS GLU SEQRES 14 B 315 LYS GLY VAL LYS PRO ASP VAL VAL THR TYR ASN THR LEU SEQRES 15 B 315 ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA SEQRES 16 B 315 LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS SEQRES 17 B 315 PRO ASP VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU SEQRES 18 B 315 ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE SEQRES 19 B 315 GLU GLU MET LYS GLU LYS GLY VAL LYS PRO ASP VAL VAL SEQRES 20 B 315 THR TYR ASN THR LEU ILE ASP GLY LEU ALA LYS ALA GLY SEQRES 21 B 315 ARG LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS SEQRES 22 B 315 GLU LYS GLY VAL LYS PRO ASP VAL VAL THR TYR ASN THR SEQRES 23 B 315 LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU SEQRES 24 B 315 ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL SEQRES 25 B 315 LYS PRO ASP SEQRES 1 C 315 VAL VAL THR TYR THR THR LEU ILE ASP GLY LEU ALA LYS SEQRES 2 C 315 ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN GLU SEQRES 3 C 315 MET LYS GLU LYS GLY VAL LYS PRO ASN VAL VAL THR TYR SEQRES 4 C 315 THR THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU SEQRES 5 C 315 GLU GLU ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS SEQRES 6 C 315 GLY VAL LYS PRO ASN VAL VAL THR TYR THR THR LEU ILE SEQRES 7 C 315 ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU SEQRES 8 C 315 GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS PRO SEQRES 9 C 315 ASN VAL VAL THR TYR THR THR LEU ILE ASP GLY LEU ALA SEQRES 10 C 315 LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN SEQRES 11 C 315 GLU MET LYS GLU LYS GLY VAL LYS PRO ASN VAL VAL THR SEQRES 12 C 315 TYR THR THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG SEQRES 13 C 315 LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS GLU SEQRES 14 C 315 LYS GLY VAL LYS PRO ASN VAL VAL THR TYR THR THR LEU SEQRES 15 C 315 ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA SEQRES 16 C 315 LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS SEQRES 17 C 315 PRO ASN VAL VAL THR TYR THR THR LEU ILE ASP GLY LEU SEQRES 18 C 315 ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE SEQRES 19 C 315 GLU GLU MET LYS GLU LYS GLY VAL LYS PRO ASN VAL VAL SEQRES 20 C 315 THR TYR THR THR LEU ILE ASP GLY LEU ALA LYS ALA GLY SEQRES 21 C 315 ARG LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS SEQRES 22 C 315 GLU LYS GLY VAL LYS PRO ASN VAL VAL THR TYR THR THR SEQRES 23 C 315 LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU SEQRES 24 C 315 ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL SEQRES 25 C 315 LYS PRO ASN SEQRES 1 D 315 VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU ALA LYS SEQRES 2 D 315 ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN GLU SEQRES 3 D 315 MET LYS GLU LYS GLY VAL LYS PRO SER VAL VAL THR TYR SEQRES 4 D 315 ASN THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU SEQRES 5 D 315 GLU GLU ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS SEQRES 6 D 315 GLY VAL LYS PRO SER VAL VAL THR TYR ASN THR LEU ILE SEQRES 7 D 315 ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU SEQRES 8 D 315 GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS PRO SEQRES 9 D 315 SER VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU ALA SEQRES 10 D 315 LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE GLN SEQRES 11 D 315 GLU MET LYS GLU LYS GLY VAL LYS PRO SER VAL VAL THR SEQRES 12 D 315 TYR ASN THR LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG SEQRES 13 D 315 LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS GLU SEQRES 14 D 315 LYS GLY VAL LYS PRO SER VAL VAL THR TYR ASN THR LEU SEQRES 15 D 315 ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU ALA SEQRES 16 D 315 LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL LYS SEQRES 17 D 315 PRO SER VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU SEQRES 18 D 315 ALA LYS ALA GLY ARG LEU GLU GLU ALA LEU GLN LEU PHE SEQRES 19 D 315 GLU GLU MET LYS GLU LYS GLY VAL LYS PRO SER VAL VAL SEQRES 20 D 315 THR TYR ASN THR LEU ILE ASP GLY LEU ALA LYS ALA GLY SEQRES 21 D 315 ARG LEU GLU GLU ALA LEU GLN LEU PHE GLU GLU MET LYS SEQRES 22 D 315 GLU LYS GLY VAL LYS PRO SER VAL VAL THR TYR ASN THR SEQRES 23 D 315 LEU ILE ASP GLY LEU ALA LYS ALA GLY ARG LEU GLU GLU SEQRES 24 D 315 ALA LEU GLN LEU PHE GLN GLU MET LYS GLU LYS GLY VAL SEQRES 25 D 315 LYS PRO SER SEQRES 1 F 9 G G G G G G G G G SEQRES 1 G 9 U U U U U U U U U SEQRES 1 H 9 A A A A A A A A A SEQRES 1 I 9 C C C C C C C C C FORMUL 9 HOH *214(H2 O) HELIX 1 AA1 VAL A 5 ALA A 18 1 14 HELIX 2 AA2 ARG A 20 LYS A 34 1 15 HELIX 3 AA3 ASP A 39 ALA A 53 1 15 HELIX 4 AA4 ARG A 55 LYS A 69 1 15 HELIX 5 AA5 ASP A 74 ALA A 88 1 15 HELIX 6 AA6 ARG A 90 LYS A 104 1 15 HELIX 7 AA7 ASP A 109 ALA A 123 1 15 HELIX 8 AA8 ARG A 125 LYS A 139 1 15 HELIX 9 AA9 ASP A 144 ALA A 158 1 15 HELIX 10 AB1 ARG A 160 LYS A 174 1 15 HELIX 11 AB2 ASP A 179 ALA A 193 1 15 HELIX 12 AB3 ARG A 195 LYS A 209 1 15 HELIX 13 AB4 ASP A 214 ALA A 228 1 15 HELIX 14 AB5 ARG A 230 LYS A 244 1 15 HELIX 15 AB6 ASP A 249 ALA A 263 1 15 HELIX 16 AB7 ARG A 265 LYS A 279 1 15 HELIX 17 AB8 ASP A 284 ALA A 298 1 15 HELIX 18 AB9 ARG A 300 LYS A 314 1 15 HELIX 19 AC1 VAL B 6 ALA B 18 1 13 HELIX 20 AC2 ARG B 20 LYS B 34 1 15 HELIX 21 AC3 ASP B 39 ALA B 53 1 15 HELIX 22 AC4 ARG B 55 LYS B 69 1 15 HELIX 23 AC5 ASP B 74 ALA B 88 1 15 HELIX 24 AC6 ARG B 90 LYS B 104 1 15 HELIX 25 AC7 ASP B 109 ALA B 123 1 15 HELIX 26 AC8 ARG B 125 LYS B 139 1 15 HELIX 27 AC9 ASP B 144 ALA B 158 1 15 HELIX 28 AD1 ARG B 160 LYS B 174 1 15 HELIX 29 AD2 ASP B 179 ALA B 193 1 15 HELIX 30 AD3 ARG B 195 LYS B 209 1 15 HELIX 31 AD4 ASP B 214 ALA B 228 1 15 HELIX 32 AD5 ARG B 230 LYS B 244 1 15 HELIX 33 AD6 ASP B 249 ALA B 263 1 15 HELIX 34 AD7 ARG B 265 LYS B 279 1 15 HELIX 35 AD8 ASP B 284 ALA B 298 1 15 HELIX 36 AD9 ARG B 300 LYS B 314 1 15 HELIX 37 AE1 VAL C 6 ALA C 18 1 13 HELIX 38 AE2 ARG C 20 LYS C 34 1 15 HELIX 39 AE3 ASN C 39 ALA C 53 1 15 HELIX 40 AE4 ARG C 55 LYS C 69 1 15 HELIX 41 AE5 ASN C 74 ALA C 88 1 15 HELIX 42 AE6 ARG C 90 LYS C 104 1 15 HELIX 43 AE7 ASN C 109 ALA C 123 1 15 HELIX 44 AE8 ARG C 125 LYS C 139 1 15 HELIX 45 AE9 ASN C 144 ALA C 158 1 15 HELIX 46 AF1 ARG C 160 LYS C 174 1 15 HELIX 47 AF2 ASN C 179 ALA C 193 1 15 HELIX 48 AF3 ARG C 195 LYS C 209 1 15 HELIX 49 AF4 ASN C 214 ALA C 228 1 15 HELIX 50 AF5 ARG C 230 LYS C 244 1 15 HELIX 51 AF6 ASN C 249 ALA C 263 1 15 HELIX 52 AF7 ARG C 265 LYS C 279 1 15 HELIX 53 AF8 ASN C 284 ALA C 298 1 15 HELIX 54 AF9 ARG C 300 LYS C 314 1 15 HELIX 55 AG1 VAL D 6 ALA D 18 1 13 HELIX 56 AG2 ARG D 20 LYS D 34 1 15 HELIX 57 AG3 SER D 39 ALA D 53 1 15 HELIX 58 AG4 ARG D 55 LYS D 69 1 15 HELIX 59 AG5 SER D 74 ALA D 88 1 15 HELIX 60 AG6 ARG D 90 LYS D 104 1 15 HELIX 61 AG7 SER D 109 ALA D 123 1 15 HELIX 62 AG8 ARG D 125 LYS D 139 1 15 HELIX 63 AG9 SER D 144 ALA D 158 1 15 HELIX 64 AH1 ARG D 160 LYS D 174 1 15 HELIX 65 AH2 SER D 179 ALA D 193 1 15 HELIX 66 AH3 ARG D 195 LYS D 209 1 15 HELIX 67 AH4 SER D 214 ALA D 228 1 15 HELIX 68 AH5 ARG D 230 LYS D 244 1 15 HELIX 69 AH6 SER D 249 ALA D 263 1 15 HELIX 70 AH7 ARG D 265 LYS D 279 1 15 HELIX 71 AH8 SER D 284 ALA D 298 1 15 HELIX 72 AH9 ARG D 300 LYS D 314 1 15 CRYST1 43.347 51.647 51.972 118.12 97.21 96.00 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 0.023070 0.002426 0.004717 0.00000 SCALE2 0.000000 0.019469 0.010971 0.00000 SCALE3 0.000000 0.000000 0.022262 0.00000