HEADER RNA 21-JUN-08 3DIX TITLE CRYSTALLIZATION OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO TITLE 2 LYSINE, K+ ANOMALOUS DATA 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, POTASSIUM CATION, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.A.SERGANOV REVDAT 5 30-AUG-23 3DIX 1 REMARK LINK REVDAT 4 13-JUL-11 3DIX 1 VERSN REVDAT 3 24-FEB-09 3DIX 1 VERSN REVDAT 2 11-NOV-08 3DIX 1 JRNL REVDAT 1 16-SEP-08 3DIX 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. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 12821 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 670 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 899 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.3660 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3810 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 : 16 REMARK 3 SOLVENT ATOMS : 18 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) : 34.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : -1.36000 REMARK 3 B33 (A**2) : 1.27000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.332 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.267 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.791 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 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 ; 1.259 ; 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 ;10.531 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 870 ; 0.055 ; 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): 1424 ; 0.159 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2589 ; 0.266 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 120 ; 0.109 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.031 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 31 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 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 ; 0.161 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7 ; 0.245 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4444 ; 0.614 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 6562 ; 0.997 ; 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): 29.1900 -1.7160 18.6150 REMARK 3 T TENSOR REMARK 3 T11: 0.0675 T22: -0.1268 REMARK 3 T33: 0.1060 T12: 0.0753 REMARK 3 T13: 0.0104 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.9185 L22: 3.8597 REMARK 3 L33: 4.8619 L12: 1.1495 REMARK 3 L13: 0.7498 L23: -0.7200 REMARK 3 S TENSOR REMARK 3 S11: 0.0947 S12: 0.3354 S13: -0.2012 REMARK 3 S21: -0.4619 S22: 0.0097 S23: -0.0572 REMARK 3 S31: 0.6798 S32: -0.3217 S33: -0.1045 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): 6.9510 47.4000 20.8980 REMARK 3 T TENSOR REMARK 3 T11: 0.1067 T22: -0.0327 REMARK 3 T33: 0.2977 T12: 0.1470 REMARK 3 T13: 0.0096 T23: 0.0437 REMARK 3 L TENSOR REMARK 3 L11: 1.2012 L22: 0.5405 REMARK 3 L33: 1.8642 L12: 0.0780 REMARK 3 L13: 0.6056 L23: 0.3877 REMARK 3 S TENSOR REMARK 3 S11: -0.2632 S12: 0.0661 S13: 0.5413 REMARK 3 S21: 0.0248 S22: -0.0107 S23: 0.0516 REMARK 3 S31: -0.6861 S32: -0.3749 S33: 0.2738 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): 8.4720 27.3140 10.9020 REMARK 3 T TENSOR REMARK 3 T11: -0.0953 T22: -0.0357 REMARK 3 T33: 0.1361 T12: 0.0866 REMARK 3 T13: 0.0088 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 3.6183 L22: 1.0982 REMARK 3 L33: 1.0952 L12: -1.3281 REMARK 3 L13: 1.2895 L23: -0.8592 REMARK 3 S TENSOR REMARK 3 S11: 0.1326 S12: 0.2146 S13: -0.0323 REMARK 3 S21: -0.0248 S22: -0.1174 S23: 0.1153 REMARK 3 S31: -0.1080 S32: 0.1040 S33: -0.0152 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): 29.6440 33.9390 14.7890 REMARK 3 T TENSOR REMARK 3 T11: -0.0922 T22: -0.0865 REMARK 3 T33: 0.0899 T12: 0.0800 REMARK 3 T13: 0.0132 T23: 0.0342 REMARK 3 L TENSOR REMARK 3 L11: 4.4933 L22: 1.7068 REMARK 3 L33: 1.3061 L12: -1.7309 REMARK 3 L13: 0.0481 L23: -0.0800 REMARK 3 S TENSOR REMARK 3 S11: 0.1125 S12: 0.4511 S13: 0.4521 REMARK 3 S21: 0.0223 S22: -0.1748 S23: -0.3431 REMARK 3 S31: -0.1626 S32: -0.0666 S33: 0.0623 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): 50.1320 8.7390 15.2870 REMARK 3 T TENSOR REMARK 3 T11: -0.0807 T22: -0.0481 REMARK 3 T33: 0.3499 T12: 0.0992 REMARK 3 T13: 0.0555 T23: 0.0656 REMARK 3 L TENSOR REMARK 3 L11: 11.2960 L22: 1.9450 REMARK 3 L33: 3.5158 L12: 1.2736 REMARK 3 L13: -1.5821 L23: 0.1060 REMARK 3 S TENSOR REMARK 3 S11: -0.4140 S12: -0.1962 S13: -1.0579 REMARK 3 S21: 0.4247 S22: -0.0614 S23: -0.5088 REMARK 3 S31: 0.3273 S32: 0.2189 S33: 0.4754 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 3DIX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-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) : 1.84 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 : 13523 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 53.43 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 27.05400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.08350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.45100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.08350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.05400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.45100 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 -0.117 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 41 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 U A 52 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 C A 104 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 122 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 U A 153 C1' - O4' - C4' ANGL. DEV. = -4.4 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 K A 200 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 O2' REMARK 620 2 G A 115 O2' 132.4 REMARK 620 3 LYS A 175 OXT 73.1 75.7 REMARK 620 N 1 2 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 75.2 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 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: 3DIY 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 3DIX A 1 174 PDB 3DIX 3DIX 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 3DIX 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 LYS A 175 10 HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETNAM LYS LYSINE FORMUL 1 CCC C9 H13 N3 O10 P2 FORMUL 2 K K 1+ FORMUL 3 NA 5(NA 1+) FORMUL 8 LYS C6 H15 N2 O2 1+ FORMUL 9 HOH *18(H2 O) LINK O3' U A 173 P CCC A 174 1555 1555 1.60 LINK O2' G A 11 K K A 200 1555 1555 2.97 LINK O6 G A 20 NA NA A 201 1555 1555 2.50 LINK N7 G A 68 NA NA A 203 1555 1555 2.95 LINK O6 G A 71 NA NA A 201 1555 1555 2.74 LINK O2' G A 115 K K A 200 1555 1555 2.97 LINK OXT LYS A 175 K K A 200 1555 1555 2.76 SITE 1 AC1 1 LYS A 175 CRYST1 54.108 78.902 140.167 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 0.018482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012674 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007134 0.00000