PDB Short entry for 5NY8 HEADER RNA 11-MAY-17 5NY8 TITLE THE STRUCTURE OF THE THERMOBIFIDA FUSCA GUANIDINE III RIBOSWITCH WITH TITLE 2 AMINOGUANIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (41-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: THERMOBIFIDA FUSCA; SOURCE 4 ORGANISM_TAXID: 2021 KEYWDS GUANIDINE III RIBOSWITCH, STEM-LOOP, PSEUDOKNOT, RNA, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,J.WANG,D.M.J.LILLEY REVDAT 3 08-MAY-24 5NY8 1 ATOM REVDAT 2 29-NOV-17 5NY8 1 JRNL REVDAT 1 18-OCT-17 5NY8 0 JRNL AUTH L.HUANG,J.WANG,T.J.WILSON,D.M.J.LILLEY JRNL TITL STRUCTURE OF THE GUANIDINE III RIBOSWITCH. JRNL REF CELL CHEM BIOL V. 24 1407 2017 JRNL REFN ESSN 2451-9456 JRNL PMID 28988949 JRNL DOI 10.1016/J.CHEMBIOL.2017.08.021 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2219: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 32303 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1605 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 25.9575 - 4.5301 0.96 2774 127 0.1484 0.2012 REMARK 3 2 4.5301 - 3.5988 0.96 2725 140 0.1485 0.1880 REMARK 3 3 3.5988 - 3.1447 0.97 2745 155 0.1554 0.1407 REMARK 3 4 3.1447 - 2.8576 0.98 2773 136 0.2224 0.2693 REMARK 3 5 2.8576 - 2.6530 0.99 2789 142 0.2940 0.3958 REMARK 3 6 2.6530 - 2.4967 0.99 2812 175 0.2903 0.3575 REMARK 3 7 2.4967 - 2.3718 0.99 2772 159 0.2812 0.3451 REMARK 3 8 2.3718 - 2.2686 0.99 2838 132 0.2757 0.3189 REMARK 3 9 2.2686 - 2.1813 1.00 2840 143 0.2933 0.3195 REMARK 3 10 2.1813 - 2.1061 0.99 2864 127 0.3217 0.3295 REMARK 3 11 2.1061 - 2.0402 1.00 2766 169 0.3227 0.3638 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.008 1980 REMARK 3 ANGLE : 1.861 3090 REMARK 3 CHIRALITY : 0.053 406 REMARK 3 PLANARITY : 0.011 83 REMARK 3 DIHEDRAL : 13.753 960 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.0499 -24.2947 -12.7480 REMARK 3 T TENSOR REMARK 3 T11: 0.4858 T22: 0.5165 REMARK 3 T33: 0.3311 T12: 0.0008 REMARK 3 T13: -0.0102 T23: 0.0308 REMARK 3 L TENSOR REMARK 3 L11: 7.9697 L22: 1.7157 REMARK 3 L33: 2.1754 L12: 2.6198 REMARK 3 L13: 0.7838 L23: 0.6492 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: -0.3038 S13: 0.1723 REMARK 3 S21: -0.0285 S22: -0.0610 S23: 0.0845 REMARK 3 S31: -0.0804 S32: 0.1043 S33: -0.0154 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.3856 -22.9860 -11.0593 REMARK 3 T TENSOR REMARK 3 T11: 0.4394 T22: 0.5157 REMARK 3 T33: 0.4169 T12: 0.0225 REMARK 3 T13: 0.0094 T23: -0.0927 REMARK 3 L TENSOR REMARK 3 L11: 5.1116 L22: 3.2855 REMARK 3 L33: 5.3292 L12: 1.8651 REMARK 3 L13: 0.2047 L23: 0.6940 REMARK 3 S TENSOR REMARK 3 S11: -0.1051 S12: -0.1154 S13: 0.3640 REMARK 3 S21: 0.2056 S22: -0.1651 S23: 0.7251 REMARK 3 S31: -0.0913 S32: -0.5298 S33: 0.3536 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8749 -31.9796 -15.9385 REMARK 3 T TENSOR REMARK 3 T11: 0.5777 T22: 0.6458 REMARK 3 T33: 0.4457 T12: -0.0515 REMARK 3 T13: -0.0101 T23: -0.0484 REMARK 3 L TENSOR REMARK 3 L11: 1.7789 L22: 1.6049 REMARK 3 L33: 0.9901 L12: 1.2958 REMARK 3 L13: 1.3845 L23: 0.8869 REMARK 3 S TENSOR REMARK 3 S11: -0.0578 S12: -0.1032 S13: -0.1228 REMARK 3 S21: 0.1273 S22: -0.1678 S23: 0.1897 REMARK 3 S31: 0.2762 S32: 0.0847 S33: 0.0576 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4272 -19.9585 -13.3757 REMARK 3 T TENSOR REMARK 3 T11: 0.4775 T22: 0.4973 REMARK 3 T33: 0.3657 T12: -0.0318 REMARK 3 T13: 0.0099 T23: 0.0337 REMARK 3 L TENSOR REMARK 3 L11: 3.1224 L22: 1.9627 REMARK 3 L33: 3.8303 L12: -0.1124 REMARK 3 L13: 0.8491 L23: 0.1366 REMARK 3 S TENSOR REMARK 3 S11: -0.1065 S12: 0.0178 S13: 0.4262 REMARK 3 S21: -0.0655 S22: -0.0513 S23: -0.0020 REMARK 3 S31: -0.1914 S32: 0.0499 S33: 0.1861 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.2887 -53.8885 -12.4929 REMARK 3 T TENSOR REMARK 3 T11: 0.4010 T22: 1.3240 REMARK 3 T33: 0.9952 T12: 0.0982 REMARK 3 T13: -0.1056 T23: -0.2529 REMARK 3 L TENSOR REMARK 3 L11: 2.2164 L22: 0.0135 REMARK 3 L33: 1.0172 L12: -0.3595 REMARK 3 L13: -1.4281 L23: 0.2558 REMARK 3 S TENSOR REMARK 3 S11: 0.0569 S12: 0.0173 S13: -1.0167 REMARK 3 S21: 0.5021 S22: 0.3712 S23: -0.9005 REMARK 3 S31: 0.1916 S32: 1.2754 S33: 0.1849 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.0401 -52.8696 -13.6412 REMARK 3 T TENSOR REMARK 3 T11: 0.4227 T22: 1.3481 REMARK 3 T33: 1.8800 T12: 0.0283 REMARK 3 T13: -0.1394 T23: -0.2801 REMARK 3 L TENSOR REMARK 3 L11: 4.1690 L22: 5.0783 REMARK 3 L33: 1.2438 L12: -4.4596 REMARK 3 L13: 1.6194 L23: -1.3890 REMARK 3 S TENSOR REMARK 3 S11: -0.0304 S12: -0.0492 S13: -0.8778 REMARK 3 S21: 0.3390 S22: 0.5980 S23: -2.3002 REMARK 3 S31: -0.3465 S32: 0.3844 S33: -0.1760 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 26 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.5310 -62.6309 -17.1940 REMARK 3 T TENSOR REMARK 3 T11: 1.2282 T22: 2.2462 REMARK 3 T33: 3.3518 T12: 0.2119 REMARK 3 T13: -0.0155 T23: -1.1126 REMARK 3 L TENSOR REMARK 3 L11: 2.4266 L22: 7.3103 REMARK 3 L33: 2.0028 L12: 1.4077 REMARK 3 L13: -2.1252 L23: -9.1043 REMARK 3 S TENSOR REMARK 3 S11: 0.0747 S12: 1.2205 S13: -2.7218 REMARK 3 S21: -2.8727 S22: 1.1769 S23: -2.2317 REMARK 3 S31: 2.6112 S32: 2.9576 S33: -0.2309 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 31 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.2621 -51.7499 -9.1451 REMARK 3 T TENSOR REMARK 3 T11: 0.4402 T22: 0.9680 REMARK 3 T33: 0.9369 T12: 0.0840 REMARK 3 T13: -0.0203 T23: 0.1300 REMARK 3 L TENSOR REMARK 3 L11: 5.0424 L22: 5.2466 REMARK 3 L33: 7.2770 L12: -0.9108 REMARK 3 L13: 1.5403 L23: -0.0698 REMARK 3 S TENSOR REMARK 3 S11: -0.0324 S12: -0.6942 S13: -0.9218 REMARK 3 S21: 0.5739 S22: 0.0570 S23: -1.0981 REMARK 3 S31: 0.1770 S32: 0.7376 S33: -0.1502 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 5NY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200004925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92019 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32303 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 25.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.640 REMARK 200 R MERGE (I) : 0.04880 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 1.02300 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1MSODIUM CHLORIDE, 0.02M MAGNESIUM REMARK 280 CHLORIDE HEXAHYDRATE, 0.05M BISTRIS7.0, 30% V/VMPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 22.11000 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 44.22000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.22000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.11000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 205 LIES ON A SPECIAL POSITION. 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 O3' G A 38 O3P CBV A 39 0.38 REMARK 500 HO2' G A 4 H5' G A 29 1.03 REMARK 500 O2' G A 4 H5' G A 29 1.06 REMARK 500 HO2' G A 29 O HOH A 202 1.55 REMARK 500 C3' G A 38 O3P CBV A 39 1.79 REMARK 500 O HOH A 217 O HOH A 219 2.06 REMARK 500 O HOH A 210 O HOH A 214 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 HO2' G B 7 H41 C B 26 2435 1.24 REMARK 500 HO2' G B 7 N4 C B 26 2435 1.47 REMARK 500 O2' G B 7 N4 C B 26 2435 2.01 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 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 G A 14 N1 - C6 - O6 ANGL. DEV. = 4.1 DEGREES REMARK 500 G A 17 C5 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 G A 38 N3 - C2 - N2 ANGL. DEV. = -4.8 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 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 30 OP2 REMARK 620 2 C A 31 OP2 94.0 REMARK 620 3 HOH A 204 O 87.3 83.3 REMARK 620 4 HOH A 216 O 170.9 93.1 87.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AGU A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G B 38 and CBV B REMARK 800 39 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV B 39 and G B REMARK 800 40 DBREF 5NY8 A 1 41 PDB 5NY8 5NY8 1 41 DBREF 5NY8 B 1 41 PDB 5NY8 5NY8 1 41 SEQRES 1 A 41 C C G G A C G A G G U G C SEQRES 2 A 41 G C C G U A C C C G G U C SEQRES 3 A 41 A G G A C A A G A C G G CBV SEQRES 4 A 41 G C SEQRES 1 B 41 C C G G A C G A G G U G C SEQRES 2 B 41 G C C G U A C C C G G U C SEQRES 3 B 41 A G G A C A A G A C G G CBV SEQRES 4 B 41 G C HET CBV A 39 33 HET CBV B 39 33 HET AGU A 101 11 HET MG A 102 1 HET MG A 103 1 HET NA A 104 1 HET MG B 101 1 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM AGU AMINOGUANIDINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 1 CBV 2(C9 H13 BR N3 O8 P) FORMUL 3 AGU C H6 N4 FORMUL 4 MG 3(MG 2+) FORMUL 6 NA NA 1+ FORMUL 8 HOH *20(H2 O) LINK O3' G A 38 P CBV A 39 1555 1555 1.63 LINK O3' CBV A 39 P G A 40 1555 1555 1.60 LINK O3' G B 38 P CBV B 39 1555 1555 1.60 LINK O3' CBV B 39 P G B 40 1555 1555 1.59 LINK O6 G A 12 NA NA A 104 1555 1555 2.81 LINK OP2 A A 30 MG MG A 102 1555 1555 2.01 LINK OP2 C A 31 MG MG A 102 1555 1555 1.85 LINK MG MG A 102 O HOH A 204 1555 1555 2.10 LINK MG MG A 102 O HOH A 216 1555 1555 2.07 LINK MG MG A 103 O HOH A 218 1555 1555 1.80 SITE 1 AC1 5 C A 6 G A 7 A A 8 C A 16 SITE 2 AC1 5 G A 17 SITE 1 AC2 4 A A 30 C A 31 HOH A 204 HOH A 216 SITE 1 AC3 1 HOH A 218 SITE 1 AC4 2 U A 11 G A 12 SITE 1 AC5 1 U B 11 SITE 1 AC6 7 G B 10 U B 11 G B 14 C B 15 SITE 2 AC6 7 C B 16 G B 37 G B 40 SITE 1 AC7 7 U B 11 G B 12 C B 13 G B 14 SITE 2 AC7 7 C B 15 G B 38 C B 41 CRYST1 83.390 83.390 66.330 90.00 90.00 120.00 P 31 2 1 12 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 0.011992 0.006923 0.000000 0.00000 SCALE2 0.000000 0.013847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015076 0.00000