HEADER RNA 31-MAR-10 3MEI TITLE REGULATORY MOTIF FROM THE THYMIDYLATE SYNTHASE MRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*CP*GP*CP*CP*GP*CP*GP*CP*CP*AP*(5BU) COMPND 3 P*GP*CP*CP*UP*GP*UP*GP*GP*CP*GP*G)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS S-TURN, C-C BASE PAIR, RNA EXPDTA X-RAY DIFFRACTION AUTHOR S.DIBROV,J.MCLEAN,T.HERMANN REVDAT 5 21-FEB-24 3MEI 1 REMARK LINK REVDAT 4 17-JUL-19 3MEI 1 REMARK LINK REVDAT 3 08-NOV-17 3MEI 1 REMARK REVDAT 2 21-MAR-12 3MEI 1 JRNL VERSN REVDAT 1 26-JAN-11 3MEI 0 JRNL AUTH S.DIBROV,J.MCLEAN,T.HERMANN JRNL TITL STRUCTURE OF AN RNA DIMER OF A REGULATORY ELEMENT FROM HUMAN JRNL TITL 2 THYMIDYLATE SYNTHASE MRNA. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 97 2011 JRNL REFN ISSN 0907-4449 JRNL PMID 21245530 JRNL DOI 10.1107/S0907444910050900 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 13933 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 640 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 28.2000 - 3.3640 0.99 2715 147 0.1500 0.1840 REMARK 3 2 3.3640 - 2.6710 1.00 2760 119 0.1680 0.2500 REMARK 3 3 2.6710 - 2.3330 1.00 2748 130 0.2080 0.3060 REMARK 3 4 2.3330 - 2.1200 0.99 2728 128 0.2210 0.2370 REMARK 3 5 2.1200 - 1.9680 0.86 2342 116 0.2310 0.3440 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 45.83 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47700 REMARK 3 B22 (A**2) : 0.74300 REMARK 3 B33 (A**2) : -1.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.31000 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 : 0.015 1084 REMARK 3 ANGLE : 2.280 1688 REMARK 3 CHIRALITY : 0.101 226 REMARK 3 PLANARITY : 0.011 46 REMARK 3 DIHEDRAL : 16.715 456 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 6.6207 -1.5441 52.1066 REMARK 3 T TENSOR REMARK 3 T11: 0.2264 T22: 0.2542 REMARK 3 T33: 0.2018 T12: 0.0092 REMARK 3 T13: -0.0264 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.1938 L22: -0.1092 REMARK 3 L33: 0.4878 L12: -0.0150 REMARK 3 L13: 0.0823 L23: 0.0634 REMARK 3 S TENSOR REMARK 3 S11: 0.0066 S12: -0.0451 S13: 0.1938 REMARK 3 S21: -0.0182 S22: 0.1467 S23: -0.0022 REMARK 3 S31: 0.1192 S32: -0.0055 S33: -0.1084 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 3MEI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 173.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9197 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13933 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.15400 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: SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.28200 REMARK 290 SMTRY3 2 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: 4110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 A 81 O HOH A 110 1.96 REMARK 500 O HOH A 122 O HOH A 127 2.14 REMARK 500 O HOH A 107 O HOH B 36 2.15 REMARK 500 O HOH A 34 O HOH A 76 2.18 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 G A 3 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 C A 10 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 A A 11 C6 - N1 - C2 ANGL. DEV. = 4.2 DEGREES REMARK 500 A A 11 N1 - C2 - N3 ANGL. DEV. = -4.7 DEGREES REMARK 500 A A 11 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 A A 11 C8 - N9 - C4 ANGL. DEV. = 2.8 DEGREES REMARK 500 U A 16 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 G A 20 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 G A 20 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 C B 5 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 C B 7 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 G B 8 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 C B 15 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 U B 16 O5' - C5' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 U B 16 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 G B 17 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 U B 18 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES 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 A 24 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 31 O REMARK 620 2 HOH A 33 O 84.1 REMARK 620 3 HOH A 131 O 95.0 80.3 REMARK 620 4 HOH B 27 O 73.0 86.1 162.9 REMARK 620 5 HOH B 28 O 158.0 87.2 103.4 86.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 25 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 26 O REMARK 620 2 HOH A 109 O 96.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 76 O REMARK 620 2 HOH B 75 O 97.5 REMARK 620 3 HOH B 106 O 157.0 66.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 26 DBREF 3MEI A 1 23 PDB 3MEI 3MEI 1 23 DBREF 3MEI B 1 23 PDB 3MEI 3MEI 1 23 SEQRES 1 A 23 C C G C C G C G C C A 5BU G SEQRES 2 A 23 C C U G U G G C G G SEQRES 1 B 23 C C G C C G C G C C A 5BU G SEQRES 2 B 23 C C U G U G G C G G MODRES 3MEI 5BU A 12 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 3MEI 5BU B 12 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE HET 5BU A 12 21 HET 5BU B 12 21 HET MG A 24 1 HET MG A 25 1 HET MG B 24 1 HET MG B 25 1 HET MG B 26 1 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 5BU 2(C9 H12 BR N2 O9 P) FORMUL 3 MG 5(MG 2+) FORMUL 8 HOH *132(H2 O) LINK O3' A A 11 P 5BU A 12 1555 1555 1.60 LINK O3' 5BU A 12 P G A 13 1555 1555 1.60 LINK O3' A B 11 P 5BU B 12 1555 1555 1.60 LINK O3' 5BU B 12 P G B 13 1555 1555 1.59 LINK MG MG A 24 O HOH A 31 1555 1555 2.12 LINK MG MG A 24 O HOH A 33 1555 1555 2.08 LINK MG MG A 24 O HOH A 131 1555 1555 2.22 LINK MG MG A 24 O HOH B 27 1555 1555 2.35 LINK MG MG A 24 O HOH B 28 1555 1555 2.07 LINK MG MG A 25 O HOH A 26 1555 1555 2.16 LINK MG MG A 25 O HOH A 109 1555 1555 1.97 LINK O HOH A 76 MG MG B 26 1555 1555 2.70 LINK MG MG B 24 O HOH B 123 1555 1555 1.97 LINK MG MG B 25 O HOH B 48 1555 1555 2.12 LINK MG MG B 26 O HOH B 75 1555 1555 2.43 LINK MG MG B 26 O HOH B 106 1555 1555 1.81 SITE 1 AC1 5 HOH A 31 HOH A 33 HOH A 131 HOH B 27 SITE 2 AC1 5 HOH B 28 SITE 1 AC2 3 G A 19 HOH A 26 HOH A 109 SITE 1 AC3 3 G B 19 G B 20 HOH B 123 SITE 1 AC4 3 G B 22 G B 23 HOH B 48 SITE 1 AC5 3 HOH A 76 HOH B 75 HOH B 106 CRYST1 32.928 38.564 41.985 90.00 100.10 90.00 P 1 21 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 0.030369 0.000000 0.005412 0.00000 SCALE2 0.000000 0.025931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024193 0.00000