HEADER RNA 20-JUN-08 3DIR TITLE CRYSTALLIZATION OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO TITLE 2 N6-1-IMINOETHYL-L-LYSINE 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 6 30-AUG-23 3DIR 1 REMARK REVDAT 5 21-OCT-20 3DIR 1 REMARK LINK REVDAT 4 13-JUL-11 3DIR 1 VERSN REVDAT 3 24-FEB-09 3DIR 1 VERSN REVDAT 2 11-NOV-08 3DIR 1 JRNL REVDAT 1 16-SEP-08 3DIR 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 (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 12823 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 688 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) : 793 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.4520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 3760 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 11 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) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): 0.346 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.264 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4220 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6583 ; 1.345 ; 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): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1843 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1481 ; 0.158 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2571 ; 0.269 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 131 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.152 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 24 ; 0.166 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.249 ; 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): NULL ; NULL ; NULL 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 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): 29.9710 -1.9400 19.0920 REMARK 3 T TENSOR REMARK 3 T11: -0.0985 T22: -0.1111 REMARK 3 T33: -0.1635 T12: 0.0630 REMARK 3 T13: -0.0852 T23: 0.0569 REMARK 3 L TENSOR REMARK 3 L11: 4.0228 L22: 7.4858 REMARK 3 L33: 3.9367 L12: 2.6166 REMARK 3 L13: 0.3586 L23: -0.2921 REMARK 3 S TENSOR REMARK 3 S11: 0.1809 S12: 0.3891 S13: -0.0901 REMARK 3 S21: -0.6788 S22: 0.1452 S23: -0.0017 REMARK 3 S31: 0.6675 S32: -0.1759 S33: -0.3261 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): 7.4670 47.2070 21.3810 REMARK 3 T TENSOR REMARK 3 T11: 0.0533 T22: 0.0852 REMARK 3 T33: 0.2408 T12: 0.1751 REMARK 3 T13: -0.0424 T23: 0.1176 REMARK 3 L TENSOR REMARK 3 L11: 1.5086 L22: 0.6686 REMARK 3 L33: 1.5506 L12: -0.0398 REMARK 3 L13: 0.6617 L23: 0.5106 REMARK 3 S TENSOR REMARK 3 S11: -0.2008 S12: 0.2212 S13: 0.7337 REMARK 3 S21: -0.1866 S22: -0.0914 S23: -0.0394 REMARK 3 S31: -0.6041 S32: -0.4139 S33: 0.2922 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): 9.0710 27.1510 11.3390 REMARK 3 T TENSOR REMARK 3 T11: -0.0197 T22: -0.0499 REMARK 3 T33: 0.0976 T12: 0.1810 REMARK 3 T13: -0.1764 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 4.4128 L22: 0.4720 REMARK 3 L33: 2.6018 L12: -1.1184 REMARK 3 L13: 1.9801 L23: -1.0703 REMARK 3 S TENSOR REMARK 3 S11: 0.0673 S12: 0.4360 S13: -0.0513 REMARK 3 S21: -0.0836 S22: -0.1890 S23: 0.3312 REMARK 3 S31: -0.3501 S32: -0.0670 S33: 0.1217 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): 30.2040 33.6440 15.5190 REMARK 3 T TENSOR REMARK 3 T11: -0.0230 T22: -0.0514 REMARK 3 T33: 0.0508 T12: 0.0757 REMARK 3 T13: -0.0563 T23: 0.0942 REMARK 3 L TENSOR REMARK 3 L11: 6.9520 L22: 5.5347 REMARK 3 L33: 1.0581 L12: -5.1300 REMARK 3 L13: 0.7134 L23: -0.0561 REMARK 3 S TENSOR REMARK 3 S11: 0.3926 S12: 0.3998 S13: 0.8504 REMARK 3 S21: -0.5336 S22: -0.2969 S23: -0.6082 REMARK 3 S31: -0.4967 S32: 0.0328 S33: -0.0958 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): 51.0780 8.5500 16.0520 REMARK 3 T TENSOR REMARK 3 T11: -0.0709 T22: 0.0362 REMARK 3 T33: 0.1834 T12: 0.1724 REMARK 3 T13: -0.0828 T23: 0.0718 REMARK 3 L TENSOR REMARK 3 L11: 12.3002 L22: 2.4438 REMARK 3 L33: 1.3254 L12: 3.1476 REMARK 3 L13: -2.2739 L23: 0.6358 REMARK 3 S TENSOR REMARK 3 S11: -0.2640 S12: -0.3562 S13: -0.8673 REMARK 3 S21: 0.3639 S22: -0.0779 S23: -0.5720 REMARK 3 S31: 0.4520 S32: 0.2165 S33: 0.3419 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 3DIR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048088. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : 13631 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 (%) : 94.3 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.5000 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 (%) : 82.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.36100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 44.50 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 (%): 54.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 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 27.40250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.65900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.41950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.65900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.40250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.41950 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 C A 95 N1 C A 95 C2 0.111 REMARK 500 C A 95 N1 C A 95 C6 0.071 REMARK 500 C A 95 C4 C A 95 C5 0.139 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. = 5.2 DEGREES REMARK 500 G A 27 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 U A 52 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 C A 95 C6 - N1 - C2 ANGL. DEV. = 3.2 DEGREES REMARK 500 C A 95 N3 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 U A 97 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 U A 153 C1' - O4' - C4' ANGL. DEV. = -5.5 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 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 OP1 REMARK 620 2 G A 11 OP2 57.2 REMARK 620 3 G A 12 O6 113.5 86.8 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 G A 20 O6 REMARK 620 2 G A 71 O6 66.6 REMARK 620 3 HOH A 308 O 71.0 57.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 203 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: 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: 3DJ0 RELATED DB: PDB REMARK 900 RELATED ID: 3DJ2 RELATED DB: PDB DBREF 3DIR A 1 174 PDB 3DIR 3DIR 1 174 SEQRES 1 A 174 GTP 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 3DIR GTP A 1 G GUANOSINE-5'-TRIPHOSPHATE MODRES 3DIR CCC A 174 C HET GTP A 1 32 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 IEL A 175 13 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETNAM IEL N~6~-[(1Z)-ETHANIMIDOYL]-L-LYSINE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 1 CCC C9 H13 N3 O10 P2 FORMUL 2 K K 1+ FORMUL 3 NA 11(NA 1+) FORMUL 14 IEL C8 H17 N3 O2 FORMUL 15 HOH *11(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.61 LINK O3' U A 173 P CCC A 174 1555 1555 1.60 LINK O6 G A 9 NA NA A 201 1555 1555 2.98 LINK OP1 G A 11 NA NA A 205 1555 1555 2.83 LINK OP2 G A 11 NA NA A 205 1555 1555 2.51 LINK O6 G A 12 NA NA A 205 1555 1555 2.74 LINK O6 G A 20 NA NA A 203 1555 1555 2.50 LINK O6 G A 69 NA NA A 204 1555 1555 2.74 LINK O6 G A 71 NA NA A 203 1555 1555 2.96 LINK O6 G A 172 NA NA A 207 1555 1555 2.59 LINK OXT IEL A 175 K K A 200 1555 1555 2.89 LINK NA NA A 203 O HOH A 308 1555 1555 2.26 SITE 1 AC2 1 HOH A 308 CRYST1 54.805 78.839 143.318 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 0.018247 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006977 0.00000 HETATM 1 PG GTP A 1 41.750 -6.355 18.003 1.00 71.62 P HETATM 2 O1G GTP A 1 42.336 -5.827 16.706 1.00 71.41 O HETATM 3 O2G GTP A 1 40.243 -6.178 17.988 1.00 71.15 O HETATM 4 O3G GTP A 1 42.344 -5.574 19.160 1.00 71.40 O HETATM 5 O3B GTP A 1 42.132 -7.929 18.172 1.00 71.04 O HETATM 6 PB GTP A 1 41.810 -9.067 17.056 1.00 71.25 P HETATM 7 O1B GTP A 1 42.351 -10.392 17.558 1.00 70.91 O HETATM 8 O2B GTP A 1 42.486 -8.708 15.744 1.00 70.93 O HETATM 9 O3A GTP A 1 40.310 -9.195 16.837 1.00 68.18 O HETATM 10 PA GTP A 1 38.894 -8.865 16.172 1.00 54.50 P HETATM 11 O1A GTP A 1 38.401 -7.462 16.134 1.00 52.70 O HETATM 12 O2A GTP A 1 38.199 -9.886 16.995 1.00 52.03 O HETATM 13 O5' GTP A 1 38.998 -9.421 14.669 1.00 48.25 O HETATM 14 C5' GTP A 1 39.636 -8.643 13.653 1.00 42.11 C HETATM 15 C4' GTP A 1 39.159 -9.031 12.265 1.00 36.88 C HETATM 16 O4' GTP A 1 39.041 -10.473 12.157 1.00 35.23 O HETATM 17 C3' GTP A 1 37.772 -8.540 11.882 1.00 34.46 C HETATM 18 O3' GTP A 1 37.766 -7.174 11.479 1.00 32.06 O HETATM 19 C2' GTP A 1 37.450 -9.477 10.723 1.00 34.03 C HETATM 20 O2' GTP A 1 38.114 -9.142 9.515 1.00 34.36 O HETATM 21 C1' GTP A 1 37.976 -10.800 11.276 1.00 33.07 C HETATM 22 N9 GTP A 1 36.952 -11.587 11.975 1.00 31.57 N HETATM 23 C8 GTP A 1 36.921 -11.927 13.310 1.00 30.93 C HETATM 24 N7 GTP A 1 35.884 -12.640 13.655 1.00 30.39 N HETATM 25 C5 GTP A 1 35.176 -12.784 12.471 1.00 30.13 C HETATM 26 C6 GTP A 1 33.959 -13.460 12.220 1.00 30.05 C HETATM 27 O6 GTP A 1 33.260 -14.077 13.030 1.00 30.90 O HETATM 28 N1 GTP A 1 33.570 -13.373 10.882 1.00 29.51 N HETATM 29 C2 GTP A 1 34.284 -12.709 9.911 1.00 29.20 C HETATM 30 N2 GTP A 1 33.771 -12.719 8.677 1.00 29.62 N HETATM 31 N3 GTP A 1 35.425 -12.073 10.132 1.00 29.44 N HETATM 32 C4 GTP A 1 35.814 -12.146 11.430 1.00 30.22 C