HEADER RNA 08-AUG-16 5SWD TITLE STRUCTURE OF THE ADENINE RIBOSWITCH APTAMER DOMAIN IN AN INTERMEDIATE- TITLE 2 BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIBRIO VULNIFICUS STRAIN 93U204 CHROMOSOME II, ADENINE COMPND 3 RIBOSWITCH APTAMER DOMAIN; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 4 ORGANISM_TAXID: 672 KEYWDS ADENINE RIBOSWITCH, PURINE RIBOSWITCH, LIGAND MIXING, INTERMEDIATE KEYWDS 2 STATE, RNA, GENE REGULATION, X-RAY FREE ELECTRON LASER EXPDTA X-RAY DIFFRACTION AUTHOR J.R.STAGNO,Y.-X.WANG,Y.LIU,Y.R.BHANDARI,C.E.CONRAD,G.NELSON,C.LI, AUTHOR 2 D.R.WENDEL,T.A.WHITE,A.BARTY,R.A.TUCKEY,N.A.ZATSEPIN,T.D.GRANT, AUTHOR 3 P.FROMME,K.TAN,X.JI,J.C.H.SPENCE REVDAT 6 04-OCT-23 5SWD 1 REMARK REVDAT 5 30-AUG-23 5SWD 1 AUTHOR JRNL REMARK LINK REVDAT 4 14-FEB-18 5SWD 1 REMARK REVDAT 3 11-OCT-17 5SWD 1 REMARK REVDAT 2 25-JAN-17 5SWD 1 JRNL REMARK REVDAT 1 23-NOV-16 5SWD 0 JRNL AUTH J.R.STAGNO,Y.LIU,Y.R.BHANDARI,C.E.CONRAD,S.PANJA,M.SWAIN, JRNL AUTH 2 L.FAN,G.NELSON,C.LI,D.R.WENDEL,T.A.WHITE,J.D.COE, JRNL AUTH 3 M.O.WIEDORN,J.KNOSKA,D.OBERTHUER,R.A.TUCKEY,P.YU,M.DYBA, JRNL AUTH 4 S.G.TARASOV,U.WEIERSTALL,T.D.GRANT,C.D.SCHWIETERS,J.ZHANG, JRNL AUTH 5 A.R.FERRE-D'AMARE,P.FROMME,D.E.DRAPER,M.LIANG,M.S.HUNTER, JRNL AUTH 6 S.BOUTET,K.TAN,X.ZUO,X.JI,A.BARTY,N.A.ZATSEPIN,H.N.CHAPMAN, JRNL AUTH 7 J.C.SPENCE,S.A.WOODSON,Y.X.WANG JRNL TITL STRUCTURES OF RIBOSWITCH RNA REACTION STATES BY JRNL TITL 2 MIX-AND-INJECT XFEL SERIAL CRYSTALLOGRAPHY. JRNL REF NATURE V. 541 242 2017 JRNL REFN ESSN 1476-4687 JRNL PMID 27841871 JRNL DOI 10.1038/NATURE20599 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 13212 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 768 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 735 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.5480 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.7350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 2826 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.73000 REMARK 3 B22 (A**2) : 2.41000 REMARK 3 B33 (A**2) : 0.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.58000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.669 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.276 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.342 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.407 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3218 ; 0.007 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5012 ; 1.524 ; 1.289 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 540 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1391 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3218 ; 5.272 ; 7.064 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 13 76 B 13 76 3441 0.050 0.050 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 13 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): -2.7437 -0.0121 28.5524 REMARK 3 T TENSOR REMARK 3 T11: 0.0941 T22: 0.1413 REMARK 3 T33: 0.1033 T12: 0.0387 REMARK 3 T13: -0.0269 T23: 0.0757 REMARK 3 L TENSOR REMARK 3 L11: 3.0175 L22: 1.3655 REMARK 3 L33: 1.1423 L12: -0.0517 REMARK 3 L13: -0.6103 L23: 0.4111 REMARK 3 S TENSOR REMARK 3 S11: 0.0841 S12: 0.5586 S13: 0.4289 REMARK 3 S21: -0.2960 S22: -0.1055 S23: 0.1040 REMARK 3 S31: -0.2571 S32: -0.1125 S33: 0.0214 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 13 B 80 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0972 -21.2493 23.2953 REMARK 3 T TENSOR REMARK 3 T11: 0.0746 T22: 0.2179 REMARK 3 T33: 0.0848 T12: 0.0071 REMARK 3 T13: -0.0078 T23: -0.1153 REMARK 3 L TENSOR REMARK 3 L11: 3.3817 L22: 1.4932 REMARK 3 L33: 0.8662 L12: -0.1576 REMARK 3 L13: -0.2733 L23: -0.3329 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: 0.7867 S13: -0.4591 REMARK 3 S21: -0.3224 S22: -0.0186 S23: 0.0152 REMARK 3 S31: 0.0843 S32: -0.0418 S33: 0.0142 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5SWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223253. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : CXI REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE CXI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3 REMARK 200 MONOCHROMATOR : KB MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : CS-PAD CXI-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.6.2 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14357 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 31.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 346.8 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 188.3 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: 5E54 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM SODIUM CACODYLATE, PH 6.5, 80 MM REMARK 280 POTASSIUM CHLORIDE, 100 MM MAGNESIUM CHLORIDE, 12 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 65% V/V (+/-)-2-METHYL-2,4-PENTANEDIOL, REMARK 280 BATCH MODE, 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 23.36000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 C A 78 REMARK 465 U A 79 REMARK 465 U A 80 REMARK 465 C A 81 REMARK 465 C A 82 REMARK 465 C A 83 REMARK 465 C B 81 REMARK 465 C B 82 REMARK 465 C B 83 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 G A 13 P G A 13 OP3 -0.122 REMARK 500 G B 13 P G B 13 OP3 -0.117 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 G A 37 OP1 REMARK 620 2 HOH A 205 O 76.1 REMARK 620 3 HOH A 206 O 103.7 73.5 REMARK 620 4 U B 68 OP1 90.5 77.5 143.4 REMARK 620 5 HOH B 204 O 166.1 92.8 80.8 78.7 REMARK 620 6 HOH B 207 O 85.7 152.5 131.7 82.3 101.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 52 OP1 REMARK 620 2 HOH A 201 O 82.5 REMARK 620 3 HOH A 207 O 109.3 72.1 REMARK 620 4 HOH B 205 O 87.4 86.7 150.5 REMARK 620 5 HOH B 206 O 152.4 75.7 80.1 74.8 REMARK 620 6 HOH B 208 O 128.6 146.5 84.2 104.7 77.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 24 OP2 REMARK 620 2 HOH B 201 O 157.5 REMARK 620 3 HOH B 202 O 73.8 84.0 REMARK 620 4 HOH B 203 O 103.0 71.0 86.7 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 ADE 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 MG B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E54 RELATED DB: PDB REMARK 900 5E54 CONTAINS THE SAME RNA IN THE LIGAND-FREE STATE REMARK 900 RELATED ID: 5SWE RELATED DB: PDB DBREF 5SWD A 13 83 PDB 5SWD 5SWD 13 83 DBREF 5SWD B 13 83 PDB 5SWD 5SWD 13 83 SEQRES 1 A 71 G G G A A G A U A U A A U SEQRES 2 A 71 C C U A A U G A U A U G G SEQRES 3 A 71 U U U G G G A G U U U C U SEQRES 4 A 71 A C C A A G A G C C U U A SEQRES 5 A 71 A A C U C U U G A U U A U SEQRES 6 A 71 C U U C C C SEQRES 1 B 71 G G G A A G A U A U A A U SEQRES 2 B 71 C C U A A U G A U A U G G SEQRES 3 B 71 U U U G G G A G U U U C U SEQRES 4 B 71 A C C A A G A G C C U U A SEQRES 5 B 71 A A C U C U U G A U U A U SEQRES 6 B 71 C U U C C C HET ADE A 101 10 HET MG A 102 1 HET MG A 103 1 HET MG B 101 1 HETNAM ADE ADENINE HETNAM MG MAGNESIUM ION FORMUL 3 ADE C5 H5 N5 FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *15(H2 O) LINK OP1 G A 37 MG MG A 102 1555 1555 2.28 LINK OP1 A A 52 MG MG A 103 1555 1555 1.80 LINK MG MG A 102 O HOH A 205 1555 1555 2.48 LINK MG MG A 102 O HOH A 206 1555 1555 2.38 LINK MG MG A 102 OP1 U B 68 1555 1555 2.26 LINK MG MG A 102 O HOH B 204 1555 1555 1.88 LINK MG MG A 102 O HOH B 207 1555 1555 1.96 LINK MG MG A 103 O HOH A 201 1555 1555 2.17 LINK MG MG A 103 O HOH A 207 1555 1555 2.55 LINK MG MG A 103 O HOH B 205 1555 1555 2.20 LINK MG MG A 103 O HOH B 206 1555 1555 2.14 LINK MG MG A 103 O HOH B 208 1555 1455 1.73 LINK OP2 A B 24 MG MG B 101 1555 1555 2.18 LINK MG MG B 101 O HOH B 201 1555 1555 2.60 LINK MG MG B 101 O HOH B 202 1555 1555 1.88 LINK MG MG B 101 O HOH B 203 1555 1555 1.90 SITE 1 AC1 7 A A 21 U A 22 U A 48 U A 49 SITE 2 AC1 7 A A 73 U A 74 HOH A 204 SITE 1 AC2 6 G A 37 HOH A 205 HOH A 206 U B 68 SITE 2 AC2 6 HOH B 204 HOH B 207 SITE 1 AC3 7 U A 51 A A 52 HOH A 201 HOH A 207 SITE 2 AC3 7 HOH B 205 HOH B 206 HOH B 208 SITE 1 AC4 4 A B 24 HOH B 201 HOH B 202 HOH B 203 CRYST1 47.910 46.720 92.250 90.00 94.06 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 0.020872 0.000000 0.001482 0.00000 SCALE2 0.000000 0.021404 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010867 0.00000