HEADER RNA 21-JUN-08 3DIY TITLE CRYSTALLIZATION OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO TITLE 2 LYSINE, MN2+ SOAK COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (174-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIBED RNA FROM THE THERMOTOGA MARITIMA SOURCE 4 MSB8 ASD GENE KEYWDS RIBOSWITCH, LYSINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.A.SERGANOV REVDAT 5 30-AUG-23 3DIY 1 REMARK LINK REVDAT 4 13-JUL-11 3DIY 1 VERSN REVDAT 3 24-FEB-09 3DIY 1 VERSN REVDAT 2 11-NOV-08 3DIY 1 JRNL REVDAT 1 16-SEP-08 3DIY 0 JRNL AUTH A.SERGANOV,L.HUANG,D.J.PATEL JRNL TITL STRUCTURAL INSIGHTS INTO AMINO ACID BINDING AND GENE CONTROL JRNL TITL 2 BY A LYSINE RIBOSWITCH. JRNL REF NATURE V. 455 1263 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18784651 JRNL DOI 10.1038/NATURE07326 REMARK 2 REMARK 2 RESOLUTION. 2.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 15510 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 822 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) : 2.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1057 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.4140 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.5450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 3756 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 37 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) : 35.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : -1.91000 REMARK 3 B33 (A**2) : 1.71000 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): 2.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.327 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.233 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.836 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4213 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6572 ; 1.239 ; 2.999 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): 4 ; 8.221 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 870 ; 0.051 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1838 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1455 ; 0.155 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2586 ; 0.265 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 137 ; 0.134 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.147 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.126 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.171 ; 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): 5 ; 0.123 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7 ; 0.312 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4450 ; 0.666 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 6565 ; 1.045 ; 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 11 REMARK 3 RESIDUE RANGE : A 163 A 174 REMARK 3 ORIGIN FOR THE GROUP (A): 29.2760 -1.9220 18.5270 REMARK 3 T TENSOR REMARK 3 T11: 0.0977 T22: -0.0557 REMARK 3 T33: 0.0023 T12: 0.0634 REMARK 3 T13: 0.0204 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.8067 L22: 4.9210 REMARK 3 L33: 5.0485 L12: 1.4330 REMARK 3 L13: 1.4091 L23: -0.6811 REMARK 3 S TENSOR REMARK 3 S11: 0.1233 S12: 0.2358 S13: -0.1968 REMARK 3 S21: -0.4825 S22: -0.0571 S23: -0.2060 REMARK 3 S31: 0.7162 S32: -0.0995 S33: -0.0662 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 : A 12 A 79 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7770 47.1370 21.3370 REMARK 3 T TENSOR REMARK 3 T11: 0.2406 T22: 0.0160 REMARK 3 T33: 0.2227 T12: 0.1548 REMARK 3 T13: -0.0324 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 1.3625 L22: 0.3026 REMARK 3 L33: 1.7578 L12: 0.3523 REMARK 3 L13: 0.7993 L23: 0.6135 REMARK 3 S TENSOR REMARK 3 S11: -0.4022 S12: -0.0440 S13: 0.6841 REMARK 3 S21: -0.0269 S22: -0.0175 S23: 0.0235 REMARK 3 S31: -0.6996 S32: -0.4138 S33: 0.4197 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 80 A 113 REMARK 3 ORIGIN FOR THE GROUP (A): 8.4070 27.1710 10.8310 REMARK 3 T TENSOR REMARK 3 T11: -0.0148 T22: -0.0015 REMARK 3 T33: 0.0223 T12: 0.0590 REMARK 3 T13: -0.0008 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 3.0855 L22: 1.3328 REMARK 3 L33: 0.6995 L12: -1.7065 REMARK 3 L13: 1.1435 L23: -0.8346 REMARK 3 S TENSOR REMARK 3 S11: 0.0802 S12: 0.1332 S13: -0.1514 REMARK 3 S21: 0.0269 S22: -0.0289 S23: 0.2007 REMARK 3 S31: -0.0810 S32: 0.0726 S33: -0.0513 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 114 A 140 REMARK 3 ORIGIN FOR THE GROUP (A): 29.6560 33.7620 14.8460 REMARK 3 T TENSOR REMARK 3 T11: -0.0249 T22: -0.0611 REMARK 3 T33: -0.0212 T12: 0.0450 REMARK 3 T13: 0.0172 T23: 0.0570 REMARK 3 L TENSOR REMARK 3 L11: 4.7922 L22: 2.7999 REMARK 3 L33: 1.6373 L12: -2.2392 REMARK 3 L13: 0.8916 L23: -0.0686 REMARK 3 S TENSOR REMARK 3 S11: 0.1151 S12: 0.4844 S13: 0.3956 REMARK 3 S21: -0.0912 S22: -0.2431 S23: -0.3034 REMARK 3 S31: -0.2298 S32: 0.0102 S33: 0.1279 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 141 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): 50.2110 8.6210 15.0630 REMARK 3 T TENSOR REMARK 3 T11: 0.0464 T22: 0.0202 REMARK 3 T33: 0.2196 T12: 0.0892 REMARK 3 T13: 0.0091 T23: 0.1362 REMARK 3 L TENSOR REMARK 3 L11: 8.6659 L22: 2.1708 REMARK 3 L33: 2.5875 L12: 1.9908 REMARK 3 L13: -2.4290 L23: 1.0429 REMARK 3 S TENSOR REMARK 3 S11: -0.3029 S12: -0.1971 S13: -1.0854 REMARK 3 S21: 0.2895 S22: -0.1811 S23: -0.5431 REMARK 3 S31: 0.4803 S32: 0.3467 S33: 0.4840 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3DIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.24 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16392 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.58800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 3DIL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 4000, 0.1M SODIUM CITRATE, 20% REMARK 280 ISOPROPANOL, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.09650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.26100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.33100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.26100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.09650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.33100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 12 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 U A 52 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 U A 153 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 U A 153 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 NA A 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 O6 REMARK 620 2 HOH A 300 O 138.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 200 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 O2' REMARK 620 2 LYS A 175 OXT 68.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 OP2 REMARK 620 2 G A 12 O6 67.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 20 O6 REMARK 620 2 G A 71 O6 76.4 REMARK 620 3 HOH A 326 O 73.0 68.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 68 N7 REMARK 620 2 G A 69 O6 88.3 REMARK 620 3 HOH A 312 O 76.2 67.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 72 OP2 REMARK 620 2 G A 73 N7 84.7 REMARK 620 3 HOH A 315 O 136.6 134.2 REMARK 620 4 HOH A 322 O 79.7 153.5 56.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 207 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 80 N7 REMARK 620 2 A A 164 OP1 93.8 REMARK 620 3 HOH A 329 O 65.5 92.3 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 K A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS A 175 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DIG RELATED DB: PDB REMARK 900 RELATED ID: 3DIL RELATED DB: PDB REMARK 900 RELATED ID: 3DIM RELATED DB: PDB REMARK 900 RELATED ID: 3DIO RELATED DB: PDB REMARK 900 RELATED ID: 3DIQ RELATED DB: PDB REMARK 900 RELATED ID: 3DIR RELATED DB: PDB REMARK 900 RELATED ID: 3DIS RELATED DB: PDB REMARK 900 RELATED ID: 3DIX RELATED DB: PDB REMARK 900 RELATED ID: 3DIZ RELATED DB: PDB REMARK 900 RELATED ID: 3DJ0 RELATED DB: PDB REMARK 900 RELATED ID: 3DJ2 RELATED DB: PDB DBREF 3DIY A 1 174 PDB 3DIY 3DIY 1 174 SEQRES 1 A 174 GDP G C C G A C G G A G G C SEQRES 2 A 174 G C G C C C G A G A U G A SEQRES 3 A 174 G U A G G C U G U C C C A SEQRES 4 A 174 U C A G G G G A G G A A U SEQRES 5 A 174 C G G G G A C G G C U G A SEQRES 6 A 174 A A G G C G A G G G C G C SEQRES 7 A 174 C G A A G G G U G C A G A SEQRES 8 A 174 G U U C C U C C C G C U C SEQRES 9 A 174 U G C A U G C C U G G G G SEQRES 10 A 174 G U A U G G G G A A U A C SEQRES 11 A 174 C C A U A C C A C U G U C SEQRES 12 A 174 A C G G A G G U C U C U C SEQRES 13 A 174 C G U G G A G A G C C G U SEQRES 14 A 174 C G G U CCC MODRES 3DIY GDP A 1 G GUANOSINE-5'-DIPHOSPHATE MODRES 3DIY CCC A 174 C HET GDP A 1 28 HET CCC A 174 23 HET K A 200 1 HET NA A 201 1 HET NA A 202 1 HET NA A 203 1 HET NA A 204 1 HET NA A 205 1 HET NA A 206 1 HET NA A 207 1 HET NA A 208 1 HET MN A 250 1 HET MN A 251 1 HET LYS A 175 10 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETNAM MN MANGANESE (II) ION HETNAM LYS LYSINE FORMUL 1 GDP C10 H15 N5 O11 P2 FORMUL 1 CCC C9 H13 N3 O10 P2 FORMUL 2 K K 1+ FORMUL 3 NA 8(NA 1+) FORMUL 11 MN 2(MN 2+) FORMUL 13 LYS C6 H15 N2 O2 1+ FORMUL 14 HOH *37(H2 O) LINK O3' GDP A 1 P G A 2 1555 1555 1.60 LINK O3' U A 173 P CCC A 174 1555 1555 1.60 LINK O6 G A 9 NA NA A 208 1555 1555 2.74 LINK O2' G A 11 K K A 200 1555 1555 2.96 LINK OP2 G A 11 NA NA A 205 1555 1555 2.84 LINK O6 G A 12 NA NA A 205 1555 1555 2.77 LINK O6 G A 20 NA NA A 201 1555 1555 2.52 LINK N7 G A 68 NA NA A 202 1555 1555 2.84 LINK O6 G A 69 NA NA A 202 1555 1555 2.93 LINK O6 G A 71 NA NA A 201 1555 1555 2.51 LINK OP2 A A 72 NA NA A 203 1555 1555 2.18 LINK N7 G A 73 NA NA A 203 1555 1555 2.86 LINK N7 G A 80 NA NA A 207 1555 1555 2.73 LINK OP1 A A 164 NA NA A 207 1555 1555 2.23 LINK OXT LYS A 175 K K A 200 1555 1555 2.78 LINK NA NA A 201 O HOH A 326 1555 1555 2.49 LINK NA NA A 202 O HOH A 312 1555 1555 2.63 LINK NA NA A 203 O HOH A 315 1555 1555 2.95 LINK NA NA A 203 O HOH A 322 1555 1555 2.81 LINK NA NA A 206 O HOH A 311 1555 1555 2.94 LINK NA NA A 207 O HOH A 329 1555 1555 2.38 LINK NA NA A 208 O HOH A 300 1555 1555 2.59 SITE 1 AC1 1 LYS A 175 SITE 1 AC2 2 HOH A 325 HOH A 326 SITE 1 AC3 1 HOH A 312 SITE 1 AC4 3 HOH A 315 HOH A 322 HOH A 323 SITE 1 AC5 1 HOH A 336 SITE 1 AC6 1 HOH A 329 SITE 1 AC7 1 HOH A 300 SITE 1 AC8 1 HOH A 331 CRYST1 54.193 78.662 140.522 90.00 90.00 90.00 P 21 21 21 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 0.018453 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007116 0.00000 HETATM 1 PB GDP A 1 40.597 -8.540 15.513 1.00 77.75 P HETATM 2 O1B GDP A 1 40.151 -7.099 15.356 1.00 77.30 O HETATM 3 O2B GDP A 1 41.615 -8.858 14.433 1.00 76.75 O HETATM 4 O3B GDP A 1 41.226 -8.730 16.882 1.00 77.11 O HETATM 5 O3A GDP A 1 39.384 -9.453 15.395 1.00 73.21 O HETATM 6 PA GDP A 1 37.842 -9.034 15.432 1.00 61.10 P HETATM 7 O1A GDP A 1 37.426 -10.291 16.105 1.00 59.02 O HETATM 8 O2A GDP A 1 37.291 -7.722 15.859 1.00 58.44 O HETATM 9 O5' GDP A 1 37.619 -9.176 13.847 1.00 55.67 O HETATM 10 C5' GDP A 1 38.170 -8.218 12.936 1.00 50.65 C HETATM 11 C4' GDP A 1 37.920 -8.594 11.486 1.00 46.39 C HETATM 12 O4' GDP A 1 37.985 -10.032 11.296 1.00 45.11 O HETATM 13 C3' GDP A 1 36.537 -8.222 10.982 1.00 44.04 C HETATM 14 O3' GDP A 1 36.488 -6.868 10.583 1.00 41.56 O HETATM 15 C2' GDP A 1 36.354 -9.188 9.819 1.00 43.64 C HETATM 16 O2' GDP A 1 37.081 -8.816 8.663 1.00 43.11 O HETATM 17 C1' GDP A 1 36.927 -10.455 10.448 1.00 43.38 C HETATM 18 N9 GDP A 1 35.974 -11.238 11.246 1.00 42.61 N HETATM 19 C8 GDP A 1 36.104 -11.567 12.575 1.00 42.12 C HETATM 20 N7 GDP A 1 35.121 -12.278 13.048 1.00 41.98 N HETATM 21 C5 GDP A 1 34.274 -12.441 11.962 1.00 41.89 C HETATM 22 C6 GDP A 1 33.038 -13.131 11.870 1.00 41.80 C HETATM 23 O6 GDP A 1 32.435 -13.746 12.760 1.00 41.89 O HETATM 24 N1 GDP A 1 32.492 -13.061 10.588 1.00 41.98 N HETATM 25 C2 GDP A 1 33.074 -12.403 9.527 1.00 41.82 C HETATM 26 N2 GDP A 1 32.403 -12.444 8.369 1.00 41.78 N HETATM 27 N3 GDP A 1 34.232 -11.753 9.598 1.00 41.85 N HETATM 28 C4 GDP A 1 34.781 -11.809 10.842 1.00 42.07 C