HEADER RNA 11-MAY-25 9OKU TITLE 16MER SELF-COMPLEMENTARY DUPLEX RNA WITH DA:S(2)U PAIR SEQUENCE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-R(*AP*GP*AP*G)-D(P*A)-R(P*AP*GP*AP*UP*CP*U)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DEOXYRIBO-PURINE, 2-THIOURIDINE, RNA DUPLEX, ORIGIN OF LIFE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR Z.FANG,J.W.SZOSTAK REVDAT 2 26-NOV-25 9OKU 1 JRNL REVDAT 1 22-OCT-25 9OKU 0 JRNL AUTH Z.FANG,O.ACIKGOZ,X.JIA,J.ESSEX,R.WEN,J.W.SZOSTAK JRNL TITL IMPACT OF 2'-DEOXYRIBO-PURINE SUBSTRATES ON NONENZYMATIC RNA JRNL TITL 2 TEMPLATE-DIRECTED PRIMER EXTENSION. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 41261857 JRNL DOI 10.1093/NAR/GKAF1228 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.FANG,O.ACIKGOZ,X.JIA,J.ESSEX,R.WEN,J.W.SZOSTAK REMARK 1 TITL IMPACT OF 2'-DEOXYRIBO-PURINE SUBSTRATES ON NONENZYMATIC RNA REMARK 1 TITL 2 TEMPLATE-DIRECTED PRIMER EXTENSION. REMARK 1 REF BIORXIV 2025 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 40909494 REMARK 1 DOI 10.1101/2025.08.29.673048 REMARK 2 REMARK 2 RESOLUTION. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7109 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) : 0.170 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.895 REMARK 3 FREE R VALUE TEST SET COUNT : 348 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 485 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 335 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.380 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 374 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 159 ; 0.029 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 572 ; 1.982 ; 1.890 REMARK 3 BOND ANGLES OTHERS (DEGREES): 386 ; 2.699 ; 1.778 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): 76 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 185 ; 0.027 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 59 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 36 ; 0.113 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 69 ; 0.143 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 137 ; 0.249 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 68 ; 0.233 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.029 ; 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): 374 ; 1.280 ; 1.282 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 375 ; 1.278 ; 1.280 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 572 ; 1.871 ; 2.337 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 573 ; 1.869 ; 2.335 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 9OKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000294997. 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 : 7122 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.479 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 : 9.400 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 (%): 38.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 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 293K 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 20.58350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 11.88389 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.52100 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 20.58350 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 11.88389 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.52100 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 20.58350 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 11.88389 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.52100 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 20.58350 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 11.88389 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.52100 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 20.58350 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 11.88389 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 41.52100 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 20.58350 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 11.88389 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 41.52100 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 23.76778 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 83.04200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 23.76778 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 83.04200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 23.76778 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 83.04200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 23.76778 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 83.04200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 23.76778 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 83.04200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 23.76778 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 83.04200 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 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 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 HOH A 218 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 250 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 268 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 276 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 286 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 288 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 292 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 301 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 N3 A A 6 O HOH A 201 2.08 REMARK 500 O HOH A 204 O HOH A 293 2.09 REMARK 500 O HOH A 221 O HOH A 293 2.16 REMARK 500 O HOH A 217 O HOH A 293 2.16 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 DA A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 A A 6 O5' - P - OP2 ANGL. DEV. = -7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 301 DISTANCE = 6.04 ANGSTROMS 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 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 16 OP1 REMARK 620 2 HOH A 205 O 163.3 REMARK 620 3 HOH A 235 O 88.1 107.7 REMARK 620 4 HOH A 271 O 92.6 89.7 101.0 REMARK 620 5 HOH A 273 O 90.7 86.4 81.9 175.6 REMARK 620 6 HOH A 279 O 88.6 75.4 175.6 81.9 95.3 REMARK 620 N 1 2 3 4 5 DBREF 9OKU A 1 16 PDB 9OKU 9OKU 1 16 SEQRES 1 A 16 A G A G DA A G A U C U SUR C SEQRES 2 A 16 U C U HET SUR A 12 20 HET MG A 101 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 MG 2+ FORMUL 3 HOH *101(H2 O) LINK O3' U A 11 P SUR A 12 1555 1555 1.62 LINK O3' SUR A 12 P C A 13 1555 1555 1.59 LINK OP1 U A 16 MG MG A 101 1555 1555 1.96 LINK MG MG A 101 O HOH A 205 1555 14654 2.21 LINK MG MG A 101 O HOH A 235 1555 1555 1.96 LINK MG MG A 101 O HOH A 271 1555 1555 2.17 LINK MG MG A 101 O HOH A 273 1555 1555 2.25 LINK MG MG A 101 O HOH A 279 1555 1555 2.41 CRYST1 41.167 41.167 124.563 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 0.024291 0.014025 0.000000 0.00000 SCALE2 0.000000 0.028049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008028 0.00000 CONECT 224 236 CONECT 236 224 237 238 239 CONECT 237 236 CONECT 238 236 CONECT 239 236 240 CONECT 240 239 241 CONECT 241 240 242 243 CONECT 242 241 244 CONECT 243 241 246 255 CONECT 244 242 245 246 CONECT 245 244 247 248 CONECT 246 243 244 254 CONECT 247 245 249 CONECT 248 245 250 251 CONECT 249 247 252 CONECT 250 248 CONECT 251 248 252 CONECT 252 249 251 253 CONECT 253 252 CONECT 254 246 CONECT 255 243 256 CONECT 256 255 CONECT 317 337 CONECT 337 317 372 408 410 CONECT 337 416 CONECT 372 337 CONECT 408 337 CONECT 410 337 CONECT 416 337 MASTER 384 0 2 0 0 0 0 6 437 1 29 2 END