PDB Short entry for 4JNX HEADER RNA BINDING PROTEIN/RNA 16-MAR-13 4JNX TITLE CRYSTAL STRUCTURE OF RNA SILENCING SUPPRESSOR P19 COMPLEXED WITH TITLE 2 DOUBLE-HELICAL RNA 20MER PG(CUG)6C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA SILENCING SUPPRESSOR P19; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 27-149; COMPND 5 SYNONYM: 19 KDA SYMPTOM SEVERITY MODULATOR; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U COMPND 9 P*GP*C)-3'; COMPND 10 CHAIN: B, G; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: SIRNA PG(CUG)6C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOMATO BUSHY STUNT VIRUS; SOURCE 3 ORGANISM_COMMON: TBSV; SOURCE 4 ORGANISM_TAXID: 12145; SOURCE 5 GENE: ORF4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS RNA SILENCING SUPPRESSION, TRINUCLEOTIDE REPEATS, PROTEIN-RNA KEYWDS 2 COMPLEX, DIMER, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.KATORCHA,A.N.POPOV,L.MALININA REVDAT 3 20-SEP-23 4JNX 1 REMARK SEQADV LINK REVDAT 2 15-NOV-17 4JNX 1 REMARK REVDAT 1 19-MAR-14 4JNX 0 JRNL AUTH E.KATORCHA,J.TAMJAR,A.N.POPOV,L.MALININA JRNL TITL PROCRUSTEAN BED OF RNA SILENCING SUPPRESSION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 30613 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1632 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2242 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2004 REMARK 3 NUCLEIC ACID ATOMS : 844 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.18000 REMARK 3 B22 (A**2) : 12.18000 REMARK 3 B33 (A**2) : -24.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.035 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.670 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3914 ; 0.019 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 2636 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5678 ; 2.032 ; 1.621 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6158 ; 1.445 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 5.757 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;37.853 ;22.157 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 336 ;14.987 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;21.029 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.209 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3224 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 934 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 988 ; 2.198 ; 3.009 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 987 ; 2.199 ; 3.005 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1228 ; 3.006 ; 4.478 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 127 1 REMARK 3 1 D 2 D 127 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 1941 ; 1.140 ; 0.500 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B G REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 401 B 420 4 REMARK 3 1 G 401 G 420 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 B (A): 586 ; 0.030 ; 0.500 REMARK 3 MEDIUM POSITIONAL 2 B (A): 616 ; 0.030 ; 0.500 REMARK 3 MEDIUM THERMAL 2 B (A**2): 586 ; 0.460 ; 2.000 REMARK 3 MEDIUM THERMAL 2 B (A**2): 616 ; 0.570 ; 2.000 REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.500 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 127 REMARK 3 RESIDUE RANGE : D 2 D 127 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5168 32.0596 -0.0002 REMARK 3 T TENSOR REMARK 3 T11: 0.0046 T22: 0.0032 REMARK 3 T33: 0.0050 T12: -0.0029 REMARK 3 T13: 0.0032 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.1515 L22: 0.1257 REMARK 3 L33: 0.5274 L12: -0.0196 REMARK 3 L13: -0.1476 L23: 0.0887 REMARK 3 S TENSOR REMARK 3 S11: -0.0057 S12: -0.0040 S13: -0.0097 REMARK 3 S21: -0.0024 S22: -0.0078 S23: 0.0094 REMARK 3 S31: -0.0223 S32: 0.0220 S33: 0.0135 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 401 B 420 REMARK 3 RESIDUE RANGE : G 401 G 420 REMARK 3 ORIGIN FOR THE GROUP (A): 26.7515 46.3161 -0.0056 REMARK 3 T TENSOR REMARK 3 T11: 0.0624 T22: 0.0515 REMARK 3 T33: 0.1073 T12: -0.0052 REMARK 3 T13: 0.0129 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.2797 L22: 0.1218 REMARK 3 L33: 0.8090 L12: -0.0971 REMARK 3 L13: 0.4039 L23: -0.2510 REMARK 3 S TENSOR REMARK 3 S11: -0.0150 S12: -0.0128 S13: 0.0582 REMARK 3 S21: -0.0083 S22: -0.0129 S23: -0.0309 REMARK 3 S31: -0.0562 S32: 0.0330 S33: 0.0279 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4JNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98035 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32285 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.72600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 1R9F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, PH 8, REMARK 280 POTASSIUM CHLORIDE, MES/NAOH, TRACE MAGNESIUM, HANGING DROP, REMARK 280 TEMPERATURE 291K, PH 6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.95850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.95680 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.45100 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 44.95850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.95680 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.45100 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 44.95850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.95680 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.45100 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.91360 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 98.90200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.91360 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 98.90200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.91360 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 98.90200 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: THE BIOLOGICAL UNIT IS A P19 HOMODIMER BOUND TO DOUBLE- REMARK 300 STRANDED RNA. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, B, G 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 420 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 425 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 462 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 ASN A 28 REMARK 465 SER A 29 REMARK 465 GLY D 1 REMARK 465 ASN D 28 REMARK 465 SER D 29 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 GLN A 31 CG CD OE1 NE2 REMARK 470 GLN D 31 CG CD OE1 NE2 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 HOH A 410 O HOH A 486 1.17 REMARK 500 N2 G B 413 O HOH B 617 1.22 REMARK 500 OP3 G B 401 O HOH B 619 1.48 REMARK 500 O6 G B 410 O HOH B 622 1.73 REMARK 500 P G B 401 O HOH B 619 1.74 REMARK 500 O HOH A 430 O HOH B 601 1.79 REMARK 500 O HOH D 452 O HOH D 487 1.91 REMARK 500 OP2 G B 401 O HOH B 619 1.94 REMARK 500 O5' G B 401 O HOH B 619 2.00 REMARK 500 OD2 ASP D 84 O HOH D 463 2.03 REMARK 500 O4' G B 401 O HOH B 615 2.05 REMARK 500 O2' C G 411 O HOH G 505 2.05 REMARK 500 O HOH D 417 O HOH D 459 2.08 REMARK 500 O HOH A 416 O HOH A 434 2.11 REMARK 500 O HOH D 440 O HOH D 469 2.14 REMARK 500 O HOH A 435 O HOH G 516 2.15 REMARK 500 CD ARG A 106 O HOH A 438 2.15 REMARK 500 O HOH D 413 O HOH D 447 2.17 REMARK 500 OE1 GLN A 120 O HOH A 474 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 423 O HOH A 467 2665 1.98 REMARK 500 O HOH A 488 O HOH D 460 5555 2.05 REMARK 500 O HOH A 422 O HOH D 444 5555 2.06 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 SER A 14 CB SER A 14 OG -0.079 REMARK 500 SER A 91 CB SER A 91 OG -0.091 REMARK 500 SER D 14 CB SER D 14 OG -0.091 REMARK 500 G B 401 P G B 401 OP3 -0.104 REMARK 500 G B 401 P G B 401 OP3 -0.125 REMARK 500 G B 416 O3' C B 417 P 0.083 REMARK 500 G G 401 P G G 401 OP3 -0.110 REMARK 500 G G 401 P G G 401 OP3 -0.130 REMARK 500 G G 416 O3' C G 417 P 0.092 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 ASP A 71 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 VAL A 97 CG1 - CB - CG2 ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP D 71 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 VAL D 97 CG1 - CB - CG2 ANGL. DEV. = 10.9 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 HIS A 3 108.27 1.49 REMARK 500 HIS D 3 109.83 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 401 O REMARK 620 2 HOH A 402 O 86.2 REMARK 620 3 HOH B 611 O 176.9 93.5 REMARK 620 4 HOH B 612 O 96.6 85.2 86.4 REMARK 620 5 HOH B 613 O 85.8 93.9 91.2 177.4 REMARK 620 6 HOH B 614 O 89.7 175.8 90.5 96.3 84.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 405 O REMARK 620 2 HOH D 406 O 178.1 REMARK 620 3 HOH D 407 O 99.2 81.7 REMARK 620 4 HOH D 408 O 82.4 96.7 178.4 REMARK 620 5 HOH D 409 O 81.5 100.0 101.5 78.7 REMARK 620 6 HOH G 504 O 92.3 86.3 77.6 102.3 173.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J39 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P19 IN COMPLEX WITH DOUBLE-HELICAL RNA 19MER REMARK 900 P(CAG)3C(CUG)3 REMARK 900 RELATED ID: 4E48 RELATED DB: PDB REMARK 900 STRUCTURE OF 20MER DOUBLE-HELICAL RNA COMPOSED OF CUG/CUG-REPEATS REMARK 900 RELATED ID: 4JGN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P19 IN COMPLEX WITH DOUBLE-HELICAL RNA 19MER REMARK 900 PUUG(CUG)5CU REMARK 900 RELATED ID: 4JK0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P19_T89Q IN COMPLEX WITH DOUBLE-HELICAL RNA REMARK 900 19MER PUUUG(CUG)5CU DBREF 4JNX A 5 127 UNP P69517 P19_TBSVK 27 149 DBREF 4JNX D 5 127 UNP P69517 P19_TBSVK 27 149 DBREF 4JNX B 401 420 PDB 4JNX 4JNX 401 420 DBREF 4JNX G 401 420 PDB 4JNX 4JNX 401 420 SEQADV 4JNX GLY A 1 UNP P69517 EXPRESSION TAG SEQADV 4JNX SER A 2 UNP P69517 EXPRESSION TAG SEQADV 4JNX HIS A 3 UNP P69517 EXPRESSION TAG SEQADV 4JNX MET A 4 UNP P69517 EXPRESSION TAG SEQADV 4JNX GLY D 1 UNP P69517 EXPRESSION TAG SEQADV 4JNX SER D 2 UNP P69517 EXPRESSION TAG SEQADV 4JNX HIS D 3 UNP P69517 EXPRESSION TAG SEQADV 4JNX MET D 4 UNP P69517 EXPRESSION TAG SEQRES 1 A 127 GLY SER HIS MET THR SER PRO PHE LYS LEU PRO ASP GLU SEQRES 2 A 127 SER PRO SER TRP THR GLU TRP ARG LEU HIS ASN ASP GLU SEQRES 3 A 127 THR ASN SER ASN GLN ASP ASN PRO LEU GLY PHE LYS GLU SEQRES 4 A 127 SER TRP GLY PHE GLY LYS VAL VAL PHE LYS ARG TYR LEU SEQRES 5 A 127 ARG TYR ASP ARG THR GLU ALA SER LEU HIS ARG VAL LEU SEQRES 6 A 127 GLY SER TRP THR GLY ASP SER VAL ASN TYR ALA ALA SER SEQRES 7 A 127 ARG PHE PHE GLY PHE ASP GLN ILE GLY CYS THR TYR SER SEQRES 8 A 127 ILE ARG PHE ARG GLY VAL SER ILE THR VAL SER GLY GLY SEQRES 9 A 127 SER ARG THR LEU GLN HIS LEU CYS GLU MET ALA ILE ARG SEQRES 10 A 127 SER LYS GLN GLU LEU LEU GLN LEU ALA PRO SEQRES 1 D 127 GLY SER HIS MET THR SER PRO PHE LYS LEU PRO ASP GLU SEQRES 2 D 127 SER PRO SER TRP THR GLU TRP ARG LEU HIS ASN ASP GLU SEQRES 3 D 127 THR ASN SER ASN GLN ASP ASN PRO LEU GLY PHE LYS GLU SEQRES 4 D 127 SER TRP GLY PHE GLY LYS VAL VAL PHE LYS ARG TYR LEU SEQRES 5 D 127 ARG TYR ASP ARG THR GLU ALA SER LEU HIS ARG VAL LEU SEQRES 6 D 127 GLY SER TRP THR GLY ASP SER VAL ASN TYR ALA ALA SER SEQRES 7 D 127 ARG PHE PHE GLY PHE ASP GLN ILE GLY CYS THR TYR SER SEQRES 8 D 127 ILE ARG PHE ARG GLY VAL SER ILE THR VAL SER GLY GLY SEQRES 9 D 127 SER ARG THR LEU GLN HIS LEU CYS GLU MET ALA ILE ARG SEQRES 10 D 127 SER LYS GLN GLU LEU LEU GLN LEU ALA PRO SEQRES 1 B 20 G C U G C U G C U G C U G SEQRES 2 B 20 C U G C U G C SEQRES 1 G 20 G C U G C U G C U G C U G SEQRES 2 G 20 C U G C U G C HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 D 301 5 HET SO4 D 302 5 HET MG D 303 1 HET MG B 501 1 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 MG 2(MG 2+) FORMUL 11 HOH *223(H2 O) HELIX 1 1 SER A 16 THR A 27 1 12 HELIX 2 2 THR A 57 GLY A 66 1 10 HELIX 3 3 THR A 69 ARG A 79 1 11 HELIX 4 4 THR A 107 GLN A 124 1 18 HELIX 5 5 SER D 16 THR D 27 1 12 HELIX 6 6 THR D 57 GLY D 66 1 10 HELIX 7 7 THR D 69 SER D 78 1 10 HELIX 8 8 ARG D 79 PHE D 81 5 3 HELIX 9 9 THR D 107 GLN D 124 1 18 SHEET 1 A 8 VAL A 46 ARG A 53 0 SHEET 2 A 8 GLY A 36 PHE A 43 -1 N GLU A 39 O ARG A 50 SHEET 3 A 8 GLY A 87 PHE A 94 -1 O THR A 89 N GLY A 42 SHEET 4 A 8 VAL A 97 GLY A 104 -1 O VAL A 101 N TYR A 90 SHEET 5 A 8 VAL D 97 GLY D 104 -1 O THR D 100 N THR A 100 SHEET 6 A 8 GLY D 87 PHE D 94 -1 N TYR D 90 O VAL D 101 SHEET 7 A 8 GLY D 36 PHE D 43 -1 N LYS D 38 O ARG D 93 SHEET 8 A 8 VAL D 46 ARG D 53 -1 O PHE D 48 N TRP D 41 LINK O HOH A 401 MG MG B 501 1555 1555 2.18 LINK O HOH A 402 MG MG B 501 1555 1555 2.09 LINK MG MG D 303 O HOH D 405 1555 1555 2.19 LINK MG MG D 303 O HOH D 406 1555 1555 2.13 LINK MG MG D 303 O HOH D 407 1555 1555 2.21 LINK MG MG D 303 O HOH D 408 1555 1555 2.25 LINK MG MG D 303 O HOH D 409 1555 1555 2.11 LINK MG MG D 303 O HOH G 504 1555 1555 2.23 LINK MG MG B 501 O HOH B 611 1555 1555 2.17 LINK MG MG B 501 O HOH B 612 1555 1555 2.20 LINK MG MG B 501 O HOH B 613 1555 1555 2.24 LINK MG MG B 501 O HOH B 614 1555 1555 2.19 SITE 1 AC1 5 SER A 6 PHE A 48 ARG A 50 HOH A 486 SITE 2 AC1 5 HOH A 487 SITE 1 AC2 4 SER A 16 HOH A 445 HOH A 485 HIS D 62 SITE 1 AC3 3 SER D 6 PHE D 48 ARG D 50 SITE 1 AC4 3 HIS A 62 SER D 16 THR D 18 SITE 1 AC5 7 SER D 91 HOH D 405 HOH D 406 HOH D 407 SITE 2 AC5 7 HOH D 408 HOH D 409 HOH G 504 SITE 1 AC6 8 SER A 91 HOH A 401 HOH A 402 U B 412 SITE 2 AC6 8 HOH B 611 HOH B 612 HOH B 613 HOH B 614 CRYST1 89.917 89.917 148.353 90.00 90.00 120.00 H 3 18 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 0.011121 0.006421 0.000000 0.00000 SCALE2 0.000000 0.012842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006741 0.00000