HEADER RNA 05-DEC-24 9MDY TITLE 16MER SELF-COMPLEMENTARY DUPLEX RNA WITH S(2)U:A PAIR SEQUENCE 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA STRAND WITH S(2)U:A PAIR SEQUENCE 2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS 2-THIOURIDINE, NUCLEOBASE MODIFICATION, NON-CANONICAL BASE PAIR, RNA, KEYWDS 2 ORGIN OF LIFE EXPDTA X-RAY DIFFRACTION AUTHOR Z.FANG,X.JIA,J.W.SZOSTAK REVDAT 2 28-MAY-25 9MDY 1 JRNL REVDAT 1 14-MAY-25 9MDY 0 JRNL AUTH Z.FANG,X.JIA,Y.XING,J.W.SZOSTAK JRNL TITL NONENZYMATIC RNA COPYING WITH A POTENTIALLY PRIMORDIAL JRNL TITL 2 GENETIC ALPHABET. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 20122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40397670 JRNL DOI 10.1073/PNAS.2505720122 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 8856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.664 REMARK 3 FREE R VALUE TEST SET COUNT : 413 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) : 1.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 554 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 336 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.00400 REMARK 3 B22 (A**2) : -0.00400 REMARK 3 B33 (A**2) : 0.01300 REMARK 3 B12 (A**2) : -0.00200 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.069 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.108 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 375 ; 0.013 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 158 ; 0.033 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 574 ; 2.250 ; 1.890 REMARK 3 BOND ANGLES OTHERS (DEGREES): 384 ; 3.073 ; 1.786 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): 77 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 185 ; 0.029 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 59 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 38 ; 0.087 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 61 ; 0.167 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 140 ; 0.250 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 63 ; 0.223 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.079 ; 0.200 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): 375 ; 1.423 ; 1.343 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 376 ; 1.421 ; 1.342 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 574 ; 1.978 ; 2.444 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 575 ; 1.976 ; 2.442 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9MDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1000290714. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8888 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M HEPES SODIUM PH 7.5, 30% V/V POLYETHYLENE GLYCOL 400, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 20.49750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 11.83424 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 40.97333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 20.49750 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 11.83424 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 40.97333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 20.49750 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 11.83424 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 40.97333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 20.49750 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 11.83424 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.97333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 20.49750 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 11.83424 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 40.97333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 20.49750 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 11.83424 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.97333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 23.66847 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 81.94667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 23.66847 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 81.94667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 23.66847 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 81.94667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 23.66847 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 81.94667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 23.66847 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 81.94667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 23.66847 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 81.94667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 235 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 242 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 257 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 284 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 285 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 287 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 218 O HOH A 280 1.85 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 A A 3 O5' - P - OP2 ANGL. DEV. = -5.4 DEGREES REMARK 500 G A 7 O5' - P - OP2 ANGL. DEV. = -18.9 DEGREES REMARK 500 C A 10 O3' - P - OP2 ANGL. DEV. = 7.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 C A 15 0.06 SIDE CHAIN 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 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 13 O2' REMARK 620 2 C A 13 O2' 0.0 REMARK 620 3 HOH A 257 O 130.4 130.4 REMARK 620 4 HOH A 257 O 130.4 130.4 0.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 217 O REMARK 620 2 HOH A 219 O 105.5 REMARK 620 3 HOH A 248 O 90.6 91.3 REMARK 620 4 HOH A 295 O 82.7 168.7 96.4 REMARK 620 5 HOH A 299 O 171.2 83.2 90.7 88.5 REMARK 620 6 HOH A 300 O 91.1 82.4 173.6 89.9 88.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 211 O REMARK 620 2 HOH A 236 O 95.6 REMARK 620 3 HOH A 280 O 85.1 96.2 REMARK 620 4 HOH A 286 O 77.8 168.9 74.6 REMARK 620 N 1 2 3 DBREF 9MDY A 1 16 PDB 9MDY 9MDY 1 16 SEQRES 1 A 16 A G A G A A G A SUR C U U C SEQRES 2 A 16 U C U HET SUR A 9 20 HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HETNAM SUR 1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5'-PHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 SUR C9 H13 N2 O8 P S FORMUL 2 MG 3(MG 2+) FORMUL 5 HOH *100(H2 O) LINK O3' A A 8 P SUR A 9 1555 1555 1.61 LINK O3' SUR A 9 P C A 10 1555 1555 1.59 LINK O2' C A 13 MG MG A 103 1555 1555 2.59 LINK O2' C A 13 MG MG A 103 1555 2665 2.59 LINK MG MG A 101 O HOH A 217 1555 1555 2.18 LINK MG MG A 101 O HOH A 219 1555 1555 2.18 LINK MG MG A 101 O HOH A 248 1555 1555 1.94 LINK MG MG A 101 O HOH A 295 1555 1555 2.10 LINK MG MG A 101 O HOH A 299 1555 1555 1.96 LINK MG MG A 101 O HOH A 300 1555 1555 2.23 LINK MG MG A 102 O HOH A 211 1555 1555 1.87 LINK MG MG A 102 O HOH A 236 1555 1555 2.09 LINK MG MG A 102 O HOH A 280 1555 1555 2.03 LINK MG MG A 102 O HOH A 286 1555 1555 2.26 LINK MG MG A 103 O HOH A 257 1555 1555 2.98 LINK MG MG A 103 O HOH A 257 1555 2665 2.98 CRYST1 40.995 40.995 122.920 90.00 90.00 120.00 H 3 2 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 0.024393 0.014083 0.000000 0.00000 SCALE2 0.000000 0.028167 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008135 0.00000 CONECT 163 177 CONECT 177 163 178 179 180 CONECT 178 177 CONECT 179 177 CONECT 180 177 181 CONECT 181 180 182 CONECT 182 181 183 184 CONECT 183 182 185 CONECT 184 182 187 196 CONECT 185 183 186 187 CONECT 186 185 188 189 CONECT 187 184 185 195 CONECT 188 186 190 CONECT 189 186 191 192 CONECT 190 188 193 CONECT 191 189 CONECT 192 189 193 CONECT 193 190 192 194 CONECT 194 193 CONECT 195 187 CONECT 196 184 197 CONECT 197 196 CONECT 267 340 CONECT 338 357 359 388 435 CONECT 338 439 440 CONECT 339 351 376 420 426 CONECT 340 267 397 CONECT 351 339 CONECT 357 338 CONECT 359 338 CONECT 376 339 CONECT 388 338 CONECT 397 340 CONECT 420 339 CONECT 426 339 CONECT 435 338 CONECT 439 338 CONECT 440 338 MASTER 391 0 4 0 0 0 0 6 439 1 38 2 END