HEADER RNA 21-JUN-08 3DJ0 TITLE CRYSTALLIZATION OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO TITLE 2 L-4-OXALYSINE 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 LYSINE RIBSOWITCH, OXALYSINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.A.SERGANOV REVDAT 5 30-AUG-23 3DJ0 1 REMARK LINK REVDAT 4 13-JUL-11 3DJ0 1 VERSN REVDAT 3 24-FEB-09 3DJ0 1 VERSN REVDAT 2 11-NOV-08 3DJ0 1 JRNL REVDAT 1 16-SEP-08 3DJ0 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 20432 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 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) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1457 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.3560 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 3752 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 83 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) : 32.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.57000 REMARK 3 B22 (A**2) : -4.24000 REMARK 3 B33 (A**2) : 5.81000 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): 0.477 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.215 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.872 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4209 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6569 ; 1.254 ; 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): 870 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1834 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1548 ; 0.163 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2614 ; 0.265 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 216 ; 0.126 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.153 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.153 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.151 ; 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 ; 0.262 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7 ; 0.276 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4446 ; 0.638 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 6562 ; 0.946 ; 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): 29.8536 -1.8620 18.9924 REMARK 3 T TENSOR REMARK 3 T11: -0.0340 T22: -0.0321 REMARK 3 T33: -0.1759 T12: 0.0256 REMARK 3 T13: -0.0342 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 1.2704 L22: 3.3236 REMARK 3 L33: 2.4566 L12: 1.1253 REMARK 3 L13: 0.8257 L23: -0.6701 REMARK 3 S TENSOR REMARK 3 S11: 0.0346 S12: 0.2292 S13: -0.2268 REMARK 3 S21: -0.3307 S22: 0.0494 S23: -0.0902 REMARK 3 S31: 0.3361 S32: -0.2091 S33: -0.0840 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): 7.3559 47.2894 21.1976 REMARK 3 T TENSOR REMARK 3 T11: 0.0615 T22: 0.0118 REMARK 3 T33: 0.0584 T12: 0.0829 REMARK 3 T13: -0.0406 T23: 0.0290 REMARK 3 L TENSOR REMARK 3 L11: 0.7263 L22: 0.3766 REMARK 3 L33: 0.6062 L12: -0.0046 REMARK 3 L13: 0.0503 L23: 0.2541 REMARK 3 S TENSOR REMARK 3 S11: -0.0563 S12: 0.1133 S13: 0.4009 REMARK 3 S21: -0.0308 S22: -0.0552 S23: 0.0888 REMARK 3 S31: -0.2814 S32: -0.2223 S33: 0.1115 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): 8.8636 27.1939 11.3035 REMARK 3 T TENSOR REMARK 3 T11: -0.0251 T22: -0.0154 REMARK 3 T33: -0.0869 T12: 0.0593 REMARK 3 T13: -0.0553 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.9781 L22: 0.4464 REMARK 3 L33: 0.9161 L12: -0.8823 REMARK 3 L13: 0.6919 L23: -0.4838 REMARK 3 S TENSOR REMARK 3 S11: 0.0698 S12: 0.1833 S13: -0.0388 REMARK 3 S21: 0.0035 S22: -0.0726 S23: 0.1910 REMARK 3 S31: -0.1889 S32: -0.0463 S33: 0.0027 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): 29.9915 33.6243 15.4260 REMARK 3 T TENSOR REMARK 3 T11: -0.0456 T22: -0.0492 REMARK 3 T33: -0.1130 T12: 0.0216 REMARK 3 T13: -0.0168 T23: 0.0618 REMARK 3 L TENSOR REMARK 3 L11: 2.6190 L22: 1.8204 REMARK 3 L33: 0.8580 L12: -1.7188 REMARK 3 L13: 0.3304 L23: -0.0703 REMARK 3 S TENSOR REMARK 3 S11: 0.1829 S12: 0.4452 S13: 0.4021 REMARK 3 S21: -0.1332 S22: -0.2871 S23: -0.3833 REMARK 3 S31: -0.1217 S32: 0.0197 S33: 0.1043 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): 50.7391 8.6419 16.0099 REMARK 3 T TENSOR REMARK 3 T11: -0.0760 T22: 0.0281 REMARK 3 T33: 0.0655 T12: 0.0390 REMARK 3 T13: -0.0232 T23: 0.0529 REMARK 3 L TENSOR REMARK 3 L11: 4.0449 L22: 1.6463 REMARK 3 L33: 0.7731 L12: 0.4055 REMARK 3 L13: -0.2553 L23: 0.3956 REMARK 3 S TENSOR REMARK 3 S11: -0.0966 S12: -0.0573 S13: -0.4854 REMARK 3 S21: 0.2287 S22: -0.0592 S23: -0.3341 REMARK 3 S31: 0.1135 S32: 0.1743 S33: 0.1558 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 3DJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048097. 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 : 21717 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 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 (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFMAC 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 (%): 54.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 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 27.27050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.26750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.54750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.26750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.27050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.54750 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 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 1 P G A 1 OP3 -0.118 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 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 U A 52 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 U A 153 C1' - O4' - C4' ANGL. DEV. = -4.7 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 209 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 O6 REMARK 620 2 HOH A 249 O 150.5 REMARK 620 3 HOH A 294 O 73.6 123.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 OP2 REMARK 620 2 G A 12 O6 73.8 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 70.6 REMARK 620 3 HOH A 239 O 69.7 68.0 REMARK 620 4 HOH A 272 O 85.0 92.7 151.9 REMARK 620 N 1 2 3 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 95.6 REMARK 620 3 HOH A 228 O 90.8 74.0 REMARK 620 4 HOH A 245 O 82.9 65.0 137.6 REMARK 620 5 HOH A 258 O 93.1 140.6 144.2 78.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 210 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 80 N7 REMARK 620 2 A A 164 OP1 88.7 REMARK 620 3 HOH A 256 O 70.9 89.3 REMARK 620 N 1 2 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 115 O2' REMARK 620 2 OLZ A 175 OXT 72.4 REMARK 620 3 HOH A 221 O 79.8 112.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 215 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 121 O4 REMARK 620 2 G A 122 O6 76.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 212 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 274 O REMARK 620 2 HOH A 292 O 65.8 REMARK 620 N 1 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: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLZ 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: 3DIY RELATED DB: PDB REMARK 900 RELATED ID: 3DIZ RELATED DB: PDB REMARK 900 RELATED ID: 3DJ2 RELATED DB: PDB DBREF 3DJ0 A 1 174 PDB 3DJ0 3DJ0 1 174 SEQRES 1 A 174 G 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 3DJ0 CCC A 174 C 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 NA A 209 1 HET NA A 210 1 HET NA A 211 1 HET NA A 212 1 HET NA A 213 1 HET NA A 214 1 HET NA A 215 1 HET NA A 216 1 HET NA A 217 1 HET OLZ A 175 10 HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETNAM OLZ O-(2-AMINOETHYL)-L-SERINE FORMUL 1 CCC C9 H13 N3 O10 P2 FORMUL 2 K K 1+ FORMUL 3 NA 17(NA 1+) FORMUL 20 OLZ C5 H12 N2 O3 FORMUL 21 HOH *83(H2 O) LINK O3' U A 173 P CCC A 174 1555 1555 1.60 LINK O6 G A 9 NA NA A 209 1555 1555 2.71 LINK OP2 G A 11 NA NA A 204 1555 1555 2.63 LINK O6 G A 12 NA NA A 204 1555 1555 2.70 LINK O6 G A 20 NA NA A 201 1555 1555 2.65 LINK N7 G A 68 NA NA A 202 1555 1555 2.80 LINK O6 G A 69 NA NA A 202 1555 1555 2.75 LINK O6 G A 71 NA NA A 201 1555 1555 2.54 LINK N7 G A 80 NA NA A 210 1555 1555 2.75 LINK O2' G A 115 K K A 200 1555 1555 2.99 LINK O4 U A 121 NA NA A 215 1555 1555 2.67 LINK O6 G A 122 NA NA A 215 1555 1555 2.95 LINK O6 G A 125 NA NA A 216 1555 1555 2.76 LINK OP1 C A 131 NA NA A 206 1555 1555 2.49 LINK OP1 A A 164 NA NA A 210 1555 1555 2.28 LINK OXT OLZ A 175 K K A 200 1555 1555 2.81 LINK K K A 200 O HOH A 221 1555 1555 2.80 LINK NA NA A 201 O HOH A 239 1555 1555 2.57 LINK NA NA A 201 O HOH A 272 1555 1555 2.35 LINK NA NA A 202 O HOH A 228 1555 1555 2.30 LINK NA NA A 202 O HOH A 245 1555 1555 2.72 LINK NA NA A 202 O HOH A 258 1555 1555 2.15 LINK NA NA A 207 O HOH A 234 1555 1555 2.60 LINK NA NA A 208 O HOH A 266 1555 1555 2.83 LINK NA NA A 209 O HOH A 249 1555 1555 2.28 LINK NA NA A 209 O HOH A 294 1555 1555 2.63 LINK NA NA A 210 O HOH A 256 1555 1555 2.48 LINK NA NA A 212 O HOH A 274 1555 1555 2.65 LINK NA NA A 212 O HOH A 292 1555 1555 2.64 LINK NA NA A 213 O HOH A 252 1555 1555 2.81 SITE 1 AC1 1 HOH A 221 SITE 1 AC2 2 HOH A 239 HOH A 272 SITE 1 AC3 3 HOH A 228 HOH A 245 HOH A 258 SITE 1 AC7 2 HOH A 249 HOH A 294 SITE 1 AC8 1 HOH A 256 SITE 1 AC9 2 HOH A 274 HOH A 292 SITE 1 BC1 1 HOH A 252 SITE 1 BC4 1 HOH A 225 CRYST1 54.541 79.095 142.535 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 0.018335 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007016 0.00000