HEADER RNA 19-MAY-14 4PLX TITLE CRYSTAL STRUCTURE OF THE TRIPLE-HELICAL STABILITY ELEMENT AT THE 3' TITLE 2 END OF MALAT1 CAVEAT 4PLX A23 A 76 HAS WRONG CHIRALITY AT ATOM C1' COMPND MOL_ID: 1; COMPND 2 MOLECULE: CORE ENE HAIRPIN AND A-RICH TRACT FROM MALAT1; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: MALAT1 KEYWDS TRIPLE HELIX, RNA STABILITY ELEMENT, MALAT1, LONG NONCODING RNA, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.A.BROWN,D.BULKLEY,J.WANG,M.L.VALENSTEIN,T.A.YARIO,T.A.STEITZ, AUTHOR 2 J.A.STEITZ REVDAT 6 27-DEC-23 4PLX 1 REMARK REVDAT 5 25-DEC-19 4PLX 1 REMARK REVDAT 4 20-SEP-17 4PLX 1 SOURCE REMARK REVDAT 3 01-OCT-14 4PLX 1 JRNL REVDAT 2 09-JUL-14 4PLX 1 JRNL REVDAT 1 25-JUN-14 4PLX 0 JRNL AUTH J.A.BROWN,D.BULKLEY,J.WANG,M.L.VALENSTEIN,T.A.YARIO, JRNL AUTH 2 T.A.STEITZ,J.A.STEITZ JRNL TITL STRUCTURAL INSIGHTS INTO THE STABILIZATION OF MALAT1 JRNL TITL 2 NONCODING RNA BY A BIPARTITE TRIPLE HELIX. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 633 2014 JRNL REFN ESSN 1545-9985 JRNL PMID 24952594 JRNL DOI 10.1038/NSMB.2844 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 17565 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 915 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1266 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 4709 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68000 REMARK 3 B22 (A**2) : 0.68000 REMARK 3 B33 (A**2) : -2.20000 REMARK 3 B12 (A**2) : 0.68000 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): 0.418 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.343 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 42.238 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5261 ; 0.010 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 2133 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8183 ; 1.026 ; 1.350 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5213 ; 1.462 ; 3.000 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): 883 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2547 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1101 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 75 B 2 75 4629 0.13 0.05 REMARK 3 2 A 2 75 C 2 75 4457 0.13 0.05 REMARK 3 3 B 2 75 C 2 75 4414 0.14 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 : A 1 A 76 REMARK 3 ORIGIN FOR THE GROUP (A): 2.5398 65.9254 65.8105 REMARK 3 T TENSOR REMARK 3 T11: 0.1807 T22: 0.1923 REMARK 3 T33: 0.7687 T12: 0.0493 REMARK 3 T13: 0.0438 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.1060 L22: 0.5024 REMARK 3 L33: 0.1085 L12: -0.1905 REMARK 3 L13: -0.0014 L23: 0.0876 REMARK 3 S TENSOR REMARK 3 S11: -0.0877 S12: -0.0103 S13: -0.0197 REMARK 3 S21: 0.1764 S22: 0.0456 S23: 0.0520 REMARK 3 S31: 0.0938 S32: 0.0140 S33: 0.0421 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 : B 1 B 76 REMARK 3 ORIGIN FOR THE GROUP (A): -20.2980 90.9453 51.8973 REMARK 3 T TENSOR REMARK 3 T11: 0.1609 T22: 0.2381 REMARK 3 T33: 0.7126 T12: 0.0245 REMARK 3 T13: -0.0059 T23: 0.0357 REMARK 3 L TENSOR REMARK 3 L11: 0.3072 L22: 0.1416 REMARK 3 L33: 0.7919 L12: 0.1895 REMARK 3 L13: 0.0543 L23: -0.0576 REMARK 3 S TENSOR REMARK 3 S11: -0.0198 S12: 0.0779 S13: 0.1637 REMARK 3 S21: -0.0336 S22: 0.0856 S23: 0.0398 REMARK 3 S31: -0.0673 S32: -0.2296 S33: -0.0658 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 : C 1 C 76 REMARK 3 ORIGIN FOR THE GROUP (A): -77.8346 111.1784 30.4334 REMARK 3 T TENSOR REMARK 3 T11: 0.2741 T22: 0.5198 REMARK 3 T33: 0.9870 T12: 0.2819 REMARK 3 T13: 0.0141 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 1.7314 L22: 1.0370 REMARK 3 L33: 0.1838 L12: -0.8652 REMARK 3 L13: -0.5371 L23: 0.2091 REMARK 3 S TENSOR REMARK 3 S11: 0.2575 S12: 0.0961 S13: -0.2646 REMARK 3 S21: 0.0118 S22: -0.2162 S23: 0.3297 REMARK 3 S31: -0.1240 S32: -0.0534 S33: -0.0412 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 4PLX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-12; 16-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; NSLS REMARK 200 BEAMLINE : 24-ID-C; X25 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979; 1.1053, 1.1060, 1.1046 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M; DECTRIS REMARK 200 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17565 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.280 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: FOLDED RNA WAS COMBINED WITH AN EQUAL REMARK 280 VOLUME OF THE RESERVOIR SOLUTION (50 MM SODIUM CACODYLATE PH 6.5, REMARK 280 18 MM MAGNESIUM CHLORIDE, 2.5 MM SPERMINE AND 9% ISOPROPANOL), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.95333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.97667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.97667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.95333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 U B 56 REMARK 465 U B 57 REMARK 465 A B 58 REMARK 465 C C 55 REMARK 465 U C 56 REMARK 465 U C 57 REMARK 465 A C 58 REMARK 465 A C 59 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 GTP A 1 O3' G A 2 P -0.109 REMARK 500 GTP B 1 O3' G B 2 P -0.112 REMARK 500 A B 75 O3' A23 B 76 P -0.092 REMARK 500 GTP C 1 O3' G C 2 P -0.101 REMARK 500 A C 75 O3' A23 C 76 P -0.105 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 GTP A 1 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 G A 2 O3' - P - OP2 ANGL. DEV. = 9.0 DEGREES REMARK 500 A A 75 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 A23 A 76 O3' - P - OP1 ANGL. DEV. = 14.4 DEGREES REMARK 500 GTP B 1 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 G B 2 O3' - P - OP2 ANGL. DEV. = 7.5 DEGREES REMARK 500 A B 75 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 A23 B 76 O3' - P - OP1 ANGL. DEV. = 11.1 DEGREES REMARK 500 GTP C 1 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 G C 2 O3' - P - OP2 ANGL. DEV. = 24.7 DEGREES REMARK 500 G C 2 O3' - P - OP1 ANGL. DEV. = -34.0 DEGREES REMARK 500 A C 75 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 A23 C 76 O3' - P - OP2 ANGL. DEV. = -14.2 DEGREES REMARK 500 A23 C 76 O3' - P - OP1 ANGL. DEV. = 16.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 4PLX A 1 76 PDB 4PLX 4PLX 1 76 DBREF 4PLX B 1 76 PDB 4PLX 4PLX 1 76 DBREF 4PLX C 1 76 PDB 4PLX 4PLX 1 76 SEQRES 1 A 76 GTP G A A G G U U U U U C U SEQRES 2 A 76 U U U C C U G A G G C G A SEQRES 3 A 76 A A G U C U C A G G U U U SEQRES 4 A 76 U G C U U U U U G G C C U SEQRES 5 A 76 U U C U U A A A A A A A A SEQRES 6 A 76 A A A A A G C A A A A23 SEQRES 1 B 76 GTP G A A G G U U U U U C U SEQRES 2 B 76 U U U C C U G A G G C G A SEQRES 3 B 76 A A G U C U C A G G U U U SEQRES 4 B 76 U G C U U U U U G G C C U SEQRES 5 B 76 U U C U U A A A A A A A A SEQRES 6 B 76 A A A A A G C A A A A23 SEQRES 1 C 76 GTP G A A G G U U U U U C U SEQRES 2 C 76 U U U C C U G A G G C G A SEQRES 3 C 76 A A G U C U C A G G U U U SEQRES 4 C 76 U G C U U U U U G G C C U SEQRES 5 C 76 U U C U U A A A A A A A A SEQRES 6 C 76 A A A A A G C A A A A23 HET GTP A 1 32 HET A23 A 76 25 HET GTP B 1 32 HET A23 B 76 25 HET GTP C 1 32 HET A23 C 76 25 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM A23 ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE FORMUL 1 GTP 3(C10 H16 N5 O14 P3) FORMUL 1 A23 3(C10 H13 N5 O9 P2) FORMUL 4 HOH *35(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.50 LINK O3' A A 75 P A23 A 76 1555 1555 1.55 LINK O3' GTP B 1 P G B 2 1555 1555 1.50 LINK O3' A B 75 P A23 B 76 1555 1555 1.52 LINK O3' GTP C 1 P G C 2 1555 1555 1.51 LINK O3' A C 75 P A23 C 76 1555 1555 1.50 CRYST1 162.820 162.820 65.930 90.00 90.00 120.00 P 32 2 1 18 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 0.006142 0.003546 0.000000 0.00000 SCALE2 0.000000 0.007092 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015168 0.00000 HETATM 1 PG GTP A 1 29.793 47.737 66.599 1.00162.83 P ANISOU 1 PG GTP A 1 18906 18642 24322 1172 -137 -21 P HETATM 2 O1G GTP A 1 31.217 48.005 66.171 1.00172.54 O ANISOU 2 O1G GTP A 1 20072 19883 25602 1187 -183 -41 O HETATM 3 O2G GTP A 1 28.947 47.126 65.519 1.00165.18 O ANISOU 3 O2G GTP A 1 19191 18954 24615 1126 -74 -1 O HETATM 4 O3G GTP A 1 29.127 48.906 67.324 1.00 87.00 O ANISOU 4 O3G GTP A 1 9311 9033 14712 1167 -147 -18 O HETATM 5 O3B GTP A 1 29.963 46.541 67.715 1.00159.88 O ANISOU 5 O3B GTP A 1 18623 18229 23893 1225 -149 -28 O HETATM 6 PB GTP A 1 28.762 45.500 68.078 1.00139.47 P ANISOU 6 PB GTP A 1 16120 15623 21251 1221 -91 -8 P HETATM 7 O1B GTP A 1 28.611 44.531 66.918 1.00114.87 O ANISOU 7 O1B GTP A 1 12982 12521 18143 1191 -47 2 O HETATM 8 O2B GTP A 1 29.018 44.936 69.468 1.00122.66 O ANISOU 8 O2B GTP A 1 14078 13454 19073 1280 -119 -18 O HETATM 9 O3A GTP A 1 27.469 46.525 68.125 1.00 91.25 O ANISOU 9 O3A GTP A 1 10005 9524 15143 1181 -59 9 O HETATM 10 PA GTP A 1 26.306 46.457 69.265 1.00 66.79 P ANISOU 10 PA GTP A 1 6989 6396 11992 1192 -30 22 P HETATM 11 O1A GTP A 1 25.280 45.403 68.832 1.00 61.87 O ANISOU 11 O1A GTP A 1 6396 5764 11346 1164 38 42 O HETATM 12 O2A GTP A 1 26.965 46.342 70.623 1.00 77.22 O ANISOU 12 O2A GTP A 1 8376 7685 13279 1256 -78 6 O HETATM 13 O5' GTP A 1 25.616 47.922 69.195 1.00 58.83 O ANISOU 13 O5' GTP A 1 5940 5406 11007 1159 -28 28 O HETATM 14 C5' GTP A 1 26.229 49.065 69.820 1.00 54.38 C ANISOU 14 C5' GTP A 1 5359 4844 10459 1182 -84 12 C HETATM 15 C4' GTP A 1 25.249 49.801 70.741 1.00 48.50 C ANISOU 15 C4' GTP A 1 4657 4084 9687 1184 -73 21 C HETATM 16 O4' GTP A 1 24.661 48.878 71.700 1.00 48.65 O ANISOU 16 O4' GTP A 1 4771 4067 9648 1214 -44 29 O HETATM 17 C3' GTP A 1 25.958 50.885 71.605 1.00 46.98 C ANISOU 17 C3' GTP A 1 4463 3885 9503 1220 -140 1 C HETATM 18 O3' GTP A 1 25.126 52.082 71.805 1.00 45.15 O ANISOU 18 O3' GTP A 1 4217 3661 9277 1197 -131 9 O HETATM 19 C2' GTP A 1 26.029 50.227 72.951 1.00 49.11 C ANISOU 19 C2' GTP A 1 4830 4114 9715 1279 -154 -4 C HETATM 20 O2' GTP A 1 26.213 51.200 73.982 1.00 48.29 O ANISOU 20 O2' GTP A 1 4750 3996 9602 1313 -201 -17 O HETATM 21 C1' GTP A 1 24.655 49.599 72.927 1.00 52.77 C ANISOU 21 C1' GTP A 1 5339 4568 10145 1252 -77 22 C HETATM 22 N9 GTP A 1 24.138 48.861 74.148 1.00 61.78 N ANISOU 22 N9 GTP A 1 6586 5665 11221 1293 -55 29 N HETATM 23 C8 GTP A 1 23.115 49.376 74.954 1.00 70.06 C ANISOU 23 C8 GTP A 1 7683 6697 12241 1295 -27 41 C HETATM 24 N7 GTP A 1 22.769 48.488 75.925 1.00 63.83 N ANISOU 24 N7 GTP A 1 6991 5867 11393 1333 -2 48 N HETATM 25 C5 GTP A 1 23.516 47.412 75.734 1.00 69.73 C ANISOU 25 C5 GTP A 1 7753 6607 12134 1354 -12 41 C HETATM 26 C6 GTP A 1 23.607 46.150 76.429 1.00 76.90 C ANISOU 26 C6 GTP A 1 8750 7477 12991 1397 4 45 C HETATM 27 O6 GTP A 1 22.880 45.934 77.430 1.00 76.82 O ANISOU 27 O6 GTP A 1 8825 7432 12931 1422 36 57 O HETATM 28 N1 GTP A 1 24.478 45.232 75.975 1.00 86.62 N ANISOU 28 N1 GTP A 1 9973 8711 14229 1410 -15 35 N HETATM 29 C2 GTP A 1 25.274 45.481 74.871 1.00 98.37 C ANISOU 29 C2 GTP A 1 11367 10236 15772 1383 -47 22 C HETATM 30 N2 GTP A 1 26.154 44.514 74.459 1.00113.42 N ANISOU 30 N2 GTP A 1 13269 12143 17684 1399 -64 12 N HETATM 31 N3 GTP A 1 25.211 46.677 74.167 1.00 73.49 N ANISOU 31 N3 GTP A 1 8130 7121 12671 1342 -60 20 N HETATM 32 C4 GTP A 1 24.378 47.638 74.558 1.00 64.90 C ANISOU 32 C4 GTP A 1 7045 6033 11579 1327 -45 29 C