HEADER RNA 20-NOV-04 1Y26 TITLE A-RIBOSWITCH-ADENINE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIBRIO VULNIFICUS A-RIBOSWITCH; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 202511-202580; COMPND 5 SYNONYM: A-RIBOSWITCH-ADENINE COMPLEX; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 672; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PUT7; SOURCE 9 OTHER_DETAILS: IN VITRO TRANSLATION KEYWDS A-RIBOSWITCH ADENINE RECOGNITION, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.SERGANOV,Y.R.YUAN,D.J.PATEL REVDAT 4 14-FEB-24 1Y26 1 REMARK LINK REVDAT 3 13-JUL-11 1Y26 1 VERSN REVDAT 2 24-FEB-09 1Y26 1 VERSN REVDAT 1 28-DEC-04 1Y26 0 JRNL AUTH A.SERGANOV,Y.R.YUAN,O.PIKOVSKAYA,A.POLONSKAIA,L.MALININA, JRNL AUTH 2 A.T.PHAN,C.HOBARTNER,R.MICURA,R.R.BREAKER,D.J.PATEL JRNL TITL STRUCTURAL BASIS FOR DISCRIMINATIVE REGULATION OF GENE JRNL TITL 2 EXPRESSION BY ADENINE- AND GUANINE-SENSING MRNAS JRNL REF CHEM.BIOL. V. 11 1729 2004 JRNL REFN ISSN 1074-5521 JRNL PMID 15610857 JRNL DOI 10.1016/J.CHEMBIOL.2004.11.018 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 11230 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 563 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 731 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.5040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1499 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.33000 REMARK 3 B22 (A**2) : 1.66000 REMARK 3 B33 (A**2) : 1.66000 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): 0.287 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.241 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.212 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.808 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1706 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2664 ; 1.790 ; 3.000 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): 354 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 731 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 618 ; 0.157 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1015 ; 0.275 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 79 ; 0.173 ; 0.200 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): 18 ; 0.159 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.254 ; 0.200 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): 2365 ; 1.293 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2655 ; 1.745 ; 4.500 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 : X 13 X 83 REMARK 3 ORIGIN FOR THE GROUP (A): 28.2781 -19.7012 -1.0057 REMARK 3 T TENSOR REMARK 3 T11: -0.1262 T22: -0.2074 REMARK 3 T33: -0.2653 T12: -0.0111 REMARK 3 T13: 0.0214 T23: 0.0967 REMARK 3 L TENSOR REMARK 3 L11: 7.6903 L22: 5.5278 REMARK 3 L33: 2.1803 L12: -2.8787 REMARK 3 L13: -1.5970 L23: 0.5079 REMARK 3 S TENSOR REMARK 3 S11: 0.4137 S12: 0.1042 S13: 1.1639 REMARK 3 S21: -0.1629 S22: -0.3084 S23: -0.6254 REMARK 3 S31: -0.2204 S32: -0.1411 S33: -0.1053 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1Y26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000031021. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-04; 08-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : NSLS; ROTATING ANODE REMARK 200 BEAMLINE : X25; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.15; 1.5418 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11832 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.06900 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 0.9 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; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MG, PEG, PH 8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 24.82750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 77.51800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.82750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 77.51800 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 X 207 O HOH X 278 2.17 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 U X 36 O3' U X 36 C3' 0.077 REMARK 500 U X 36 C2 U X 36 O2 0.061 REMARK 500 U X 36 N1 U X 36 C6 0.071 REMARK 500 U X 36 N3 U X 36 C4 0.072 REMARK 500 G X 37 P G X 37 OP1 0.238 REMARK 500 G X 37 P G X 37 O5' 0.487 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 U X 22 C5 - C4 - O4 ANGL. DEV. = -4.0 DEGREES REMARK 500 A X 24 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 C X 26 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 C X 27 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 G X 37 O5' - P - OP1 ANGL. DEV. = 12.6 DEGREES REMARK 500 G X 37 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 G X 37 P - O5' - C5' ANGL. DEV. = -16.5 DEGREES REMARK 500 U X 41 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 U X 51 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 A X 56 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 C X 67 O5' - P - OP1 ANGL. DEV. = -7.1 DEGREES REMARK 500 C X 67 C5' - C4' - O4' ANGL. DEV. = -8.2 DEGREES REMARK 500 U X 75 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 U X 77 O4' - C1' - N1 ANGL. DEV. = 4.5 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 X 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A X 23 OP2 REMARK 620 2 HOH X 290 O 84.1 REMARK 620 3 HOH X 291 O 98.2 176.8 REMARK 620 4 HOH X 292 O 173.3 89.3 88.5 REMARK 620 5 HOH X 293 O 90.6 91.0 86.7 89.6 REMARK 620 6 HOH X 294 O 90.7 92.1 90.2 89.4 176.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A X 24 OP1 REMARK 620 2 HOH X 273 O 77.0 REMARK 620 3 HOH X 274 O 103.3 178.7 REMARK 620 4 HOH X 275 O 93.1 90.4 90.8 REMARK 620 5 HOH X 276 O 87.1 87.9 90.9 178.2 REMARK 620 6 HOH X 277 O 166.6 89.6 90.1 87.8 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH X 267 O REMARK 620 2 HOH X 268 O 175.6 REMARK 620 3 HOH X 269 O 90.6 88.5 REMARK 620 4 HOH X 270 O 88.7 92.3 179.0 REMARK 620 5 HOH X 271 O 89.9 94.4 89.5 89.7 REMARK 620 6 HOH X 272 O 90.4 85.3 92.1 88.7 178.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH X 278 O REMARK 620 2 HOH X 279 O 178.0 REMARK 620 3 HOH X 280 O 89.1 88.9 REMARK 620 4 HOH X 281 O 92.7 89.3 178.2 REMARK 620 5 HOH X 282 O 89.6 90.7 90.5 89.7 REMARK 620 6 HOH X 283 O 88.3 91.4 90.6 89.3 177.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH X 284 O REMARK 620 2 HOH X 285 O 176.4 REMARK 620 3 HOH X 286 O 91.3 92.1 REMARK 620 4 HOH X 287 O 87.7 88.9 179.0 REMARK 620 5 HOH X 288 O 89.3 89.4 89.2 90.8 REMARK 620 6 HOH X 289 O 91.9 89.5 89.2 90.7 178.1 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 MG X 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADE X 90 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y27 RELATED DB: PDB REMARK 900 G-RIBOSWITCH-GUANINE COMPLEX REMARK 999 REMARK 999 THE A-RIBOSWITCH SEQUENCE WAS DERIVED FROM THE REMARK 999 SEQUENCE LOCATED UPSTREAM OF THE ADD GENE ENCODING REMARK 999 FOR THE ADENINE DEAMINASE FROM VIBRIO VULNIFICUS. REMARK 999 THE STRUCTURE CONTAINED IN THIS ENTRY IS A REMARK 999 COMPLEX BETWEEN ADENINE AND A DOMAIN ('APTAMER REMARK 999 DOMAIN') OF THE RIBOSWITCH, WHICH STIMULATES REMARK 999 TRANSLATION OF THE ADD GENE IN RESPONSE TO THE REMARK 999 PRESENCE OF ADENINE IN THE CELL. REMARK 999 THE SEQUENCE CAN BE FOUND NATURALLY AND IT MATCHES REMARK 999 THE GENEBANK ENTRY 27358288 AE016809 OF VIBRIO REMARK 999 VULNIFICUS (RESIDUES 202511-202580). DBREF 1Y26 X 13 83 PDB 1Y26 1Y26 13 83 SEQRES 1 X 71 C G C U U C A U A U A A U SEQRES 2 X 71 C C U A A U G A U A U G G SEQRES 3 X 71 U U U G G G A G U U U C U SEQRES 4 X 71 A C C A A G A G C C U U A SEQRES 5 X 71 A A C U C U U G A U U A U SEQRES 6 X 71 G A A G U G HET MG X 101 1 HET MG X 102 1 HET MG X 103 1 HET MG X 104 1 HET MG X 105 1 HET ADE X 90 10 HETNAM MG MAGNESIUM ION HETNAM ADE ADENINE FORMUL 2 MG 5(MG 2+) FORMUL 7 ADE C5 H5 N5 FORMUL 8 HOH *94(H2 O) LINK OP2 A X 23 MG MG X 105 1555 1555 2.44 LINK OP1 A X 24 MG MG X 102 1555 1555 2.10 LINK MG MG X 101 O HOH X 267 1555 1555 2.17 LINK MG MG X 101 O HOH X 268 1555 1555 2.18 LINK MG MG X 101 O HOH X 269 1555 1555 2.17 LINK MG MG X 101 O HOH X 270 1555 1555 2.18 LINK MG MG X 101 O HOH X 271 1555 1555 2.18 LINK MG MG X 101 O HOH X 272 1555 1555 2.18 LINK MG MG X 102 O HOH X 273 1555 1555 2.18 LINK MG MG X 102 O HOH X 274 1555 1555 2.18 LINK MG MG X 102 O HOH X 275 1555 1555 2.18 LINK MG MG X 102 O HOH X 276 1555 1555 2.17 LINK MG MG X 102 O HOH X 277 1555 1555 2.18 LINK MG MG X 103 O HOH X 278 1555 1555 2.17 LINK MG MG X 103 O HOH X 279 1555 1555 2.17 LINK MG MG X 103 O HOH X 280 1555 1555 2.18 LINK MG MG X 103 O HOH X 281 1555 1555 2.18 LINK MG MG X 103 O HOH X 282 1555 1555 2.18 LINK MG MG X 103 O HOH X 283 1555 1555 2.18 LINK MG MG X 104 O HOH X 284 1555 1555 2.18 LINK MG MG X 104 O HOH X 285 1555 1555 2.18 LINK MG MG X 104 O HOH X 286 1555 1555 2.18 LINK MG MG X 104 O HOH X 287 1555 1555 2.17 LINK MG MG X 104 O HOH X 288 1555 1555 2.19 LINK MG MG X 104 O HOH X 289 1555 1555 2.18 LINK MG MG X 105 O HOH X 290 1555 1555 2.20 LINK MG MG X 105 O HOH X 291 1555 1555 2.17 LINK MG MG X 105 O HOH X 292 1555 1555 2.17 LINK MG MG X 105 O HOH X 293 1555 1555 2.18 LINK MG MG X 105 O HOH X 294 1555 1555 2.18 SITE 1 AC1 6 HOH X 267 HOH X 268 HOH X 269 HOH X 270 SITE 2 AC1 6 HOH X 271 HOH X 272 SITE 1 AC2 6 A X 24 HOH X 273 HOH X 274 HOH X 275 SITE 2 AC2 6 HOH X 276 HOH X 277 SITE 1 AC3 6 HOH X 278 HOH X 279 HOH X 280 HOH X 281 SITE 2 AC3 6 HOH X 282 HOH X 283 SITE 1 AC4 6 HOH X 284 HOH X 285 HOH X 286 HOH X 287 SITE 2 AC4 6 HOH X 288 HOH X 289 SITE 1 AC5 6 A X 23 HOH X 290 HOH X 291 HOH X 292 SITE 2 AC5 6 HOH X 293 HOH X 294 SITE 1 AC6 8 A X 21 U X 22 U X 47 U X 51 SITE 2 AC6 8 A X 52 A X 73 U X 74 U X 75 CRYST1 49.655 155.036 25.185 90.00 90.00 90.00 P 21 21 2 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 0.020139 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039706 0.00000