HEADER RNA 20-JUN-11 3SJ2 TITLE A CRYSTAL STRUCTURE OF A MODEL OF THE REPEATING R(CGG) TRANSCRIPT TITLE 2 FOUND IN FRAGILE X SYNDROME COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*UP*UP*GP*GP*GP*CP*CP*GP*GP*CP*GP*GP*CP*GP*GP*GP*UP*CP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'- COMPND 8 R(P*GP*GP*GP*CP*CP*GP*GP*CP*GP*GP*CP*GP*GP*GP*UP*CP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS TRINUCLEOTIDE DISORDERS, FRAGILE X-SYNDROME, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,F.PENGFEI,H.PARK,K.NETTLES,M.GUO,M.D.DISNEY REVDAT 3 28-FEB-24 3SJ2 1 REMARK REVDAT 2 28-SEP-11 3SJ2 1 JRNL REVDAT 1 03-AUG-11 3SJ2 0 JRNL AUTH A.KUMAR,P.FANG,H.PARK,M.GUO,K.W.NETTLES,M.D.DISNEY JRNL TITL A CRYSTAL STRUCTURE OF A MODEL OF THE REPEATING R(CGG) JRNL TITL 2 TRANSCRIPT FOUND IN FRAGILE X SYNDROME. JRNL REF CHEMBIOCHEM V. 12 2140 2011 JRNL REFN ISSN 1439-4227 JRNL PMID 21766409 JRNL DOI 10.1002/CBIC.201100337 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 22170 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.5487 - 3.2778 0.92 1593 140 0.1587 0.1560 REMARK 3 2 3.2778 - 2.6023 0.96 1626 148 0.1727 0.2152 REMARK 3 3 2.6023 - 2.2735 0.97 1622 144 0.1626 0.1820 REMARK 3 4 2.2735 - 2.0657 0.98 1633 140 0.1591 0.1971 REMARK 3 5 2.0657 - 1.9177 0.98 1628 146 0.1468 0.1821 REMARK 3 6 1.9177 - 1.8047 0.98 1621 146 0.1421 0.1791 REMARK 3 7 1.8047 - 1.7143 0.98 1628 140 0.1326 0.1567 REMARK 3 8 1.7143 - 1.6397 0.97 1602 145 0.1222 0.1818 REMARK 3 9 1.6397 - 1.5766 0.96 1594 140 0.1226 0.1617 REMARK 3 10 1.5766 - 1.5222 0.96 1592 131 0.1249 0.1882 REMARK 3 11 1.5222 - 1.4746 0.94 1523 133 0.1449 0.1717 REMARK 3 12 1.4746 - 1.4324 0.93 1569 134 0.1570 0.2356 REMARK 3 13 1.4324 - 1.3947 0.91 1472 132 0.1820 0.2734 REMARK 3 14 1.3947 - 1.3600 0.88 1467 122 0.2042 0.2560 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.65 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 39.23 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32870 REMARK 3 B22 (A**2) : -0.88030 REMARK 3 B33 (A**2) : 0.55150 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.09780 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 873 REMARK 3 ANGLE : 0.783 1358 REMARK 3 CHIRALITY : 0.054 179 REMARK 3 PLANARITY : 0.008 38 REMARK 3 DIHEDRAL : 13.802 425 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SJ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL, ASYMMETRIC REMARK 200 CUT 4.965 DEGS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24111 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 27.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM CHLORIDE, 0.01 M REMARK 280 MAGNESIUM CHLORIDE, 0.05 M TRIS.HCL, 30%(V/V)PEG 400, PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 27.83000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 27.83000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.16000 REMARK 290 SMTRY3 4 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 B 252 O HOH B 265 1.85 REMARK 500 O HOH A 96 O HOH A 140 1.86 REMARK 500 O HOH A 253 O HOH A 264 2.04 REMARK 500 O HOH B 157 O HOH B 246 2.08 REMARK 500 O HOH A 126 O HOH A 213 2.08 REMARK 500 O HOH B 186 O HOH B 243 2.13 REMARK 500 O HOH B 138 O HOH B 164 2.16 REMARK 500 O HOH B 79 O HOH B 245 2.17 REMARK 500 O HOH A 118 O HOH A 192 2.19 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 B 156 O HOH B 180 3555 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 20 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 21 DBREF 3SJ2 A 1 19 PDB 3SJ2 3SJ2 1 19 DBREF 3SJ2 B 3 19 PDB 3SJ2 3SJ2 3 19 SEQRES 1 A 19 U U G G G C C G G C G G C SEQRES 2 A 19 G G G U C C SEQRES 1 B 17 G G G C C G G C G G C G G SEQRES 2 B 17 G U C C HET ACT A 20 7 HET ACT A 21 7 HETNAM ACT ACETATE ION FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 HOH *277(H2 O) SITE 1 AC1 5 G A 15 G A 16 HOH A 56 HOH A 249 SITE 2 AC1 5 HOH B 72 SITE 1 AC2 5 G A 11 HOH A 64 G B 12 C B 13 SITE 2 AC2 5 HOH B 42 CRYST1 55.660 32.320 69.442 90.00 108.95 90.00 C 1 2 1 4 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 0.017966 0.000000 0.006170 0.00000 SCALE2 0.000000 0.030941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015226 0.00000