HEADER RNA 18-JAN-16 5HN2 TITLE BASE PAIRING AND STRUCTURE INSIGHTS INTO THE 5-FORMYLCYTOSINE IN RNA TITLE 2 DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3'); COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA, 5-FORMYLCYTOSINE EXPDTA X-RAY DIFFRACTION AUTHOR Z.P.LUO,J.SHENG REVDAT 3 27-SEP-23 5HN2 1 JRNL REMARK LINK REVDAT 2 15-JUN-16 5HN2 1 JRNL REVDAT 1 27-APR-16 5HN2 0 JRNL AUTH R.WANG,Z.LUO,K.HE,M.O.DELANEY,D.CHEN,J.SHENG JRNL TITL BASE PAIRING AND STRUCTURAL INSIGHTS INTO THE JRNL TITL 2 5-FORMYLCYTOSINE IN RNA DUPLEX. JRNL REF NUCLEIC ACIDS RES. V. 44 4968 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27079978 JRNL DOI 10.1093/NAR/GKW235 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 17551 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) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.140 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 896 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1283 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.1220 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.1910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1014 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : 0.94000 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): 0.017 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.012 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.358 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.986 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.984 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1118 ; 0.022 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 477 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1701 ; 2.518 ; 1.469 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1153 ; 2.106 ; 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): 193 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 576 ; 0.035 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 246 ; 0.022 ; 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): 1118 ; 3.731 ; 4.297 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1117 ; 3.722 ; 4.296 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1701 ; 4.328 ; 8.125 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1838 ; 4.525 ;20.033 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1748 ; 4.224 ;19.527 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1595 ; 7.077 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 62 ;24.558 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1627 ;12.603 ; 5.000 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 : BABINET MODEL WITH 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 5HN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 197D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% MPD, 50 MM TRIS-HCL (PH 7.5), 50 REMARK 280 MM NH4AC, 10 MM MGCL2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 39.09733 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 19.54867 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 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: 740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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: 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 B 111 O HOH D 103 2.13 REMARK 500 O HOH A 124 O HOH B 104 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 A A 3 O5' A A 3 C5' -0.065 REMARK 500 G A 5 C5' G A 5 C4' -0.055 REMARK 500 A A 7 O5' A A 7 C5' -0.062 REMARK 500 RSQ B 4 O3' G B 5 P 0.075 REMARK 500 A C 3 O3' RSQ C 4 P -0.097 REMARK 500 RSQ C 4 O3' G C 5 P 0.091 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. = -13.9 DEGREES REMARK 500 G A 5 C3' - C2' - C1' ANGL. DEV. = -4.4 DEGREES REMARK 500 U B 6 O5' - P - OP2 ANGL. DEV. = -7.7 DEGREES REMARK 500 A B 7 O5' - P - OP2 ANGL. DEV. = -6.1 DEGREES REMARK 500 A C 3 O5' - P - OP2 ANGL. DEV. = -6.1 DEGREES REMARK 500 RSQ C 4 O3' - P - OP2 ANGL. DEV. = 10.5 DEGREES REMARK 500 G D 5 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 A F 7 O5' - P - OP2 ANGL. DEV. = -5.9 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 G C 1 0.05 SIDE CHAIN 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 130 DISTANCE = 8.35 ANGSTROMS REMARK 525 HOH A 131 DISTANCE = 9.64 ANGSTROMS REMARK 525 HOH C 124 DISTANCE = 8.27 ANGSTROMS REMARK 525 HOH D 122 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH D 123 DISTANCE = 10.71 ANGSTROMS REMARK 525 HOH E 142 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH E 143 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH E 144 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH E 145 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH E 146 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH E 147 DISTANCE = 7.89 ANGSTROMS REMARK 525 HOH E 148 DISTANCE = 9.75 ANGSTROMS REMARK 525 HOH E 149 DISTANCE = 13.11 ANGSTROMS REMARK 525 HOH F 234 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH F 235 DISTANCE = 7.45 ANGSTROMS REMARK 525 HOH F 236 DISTANCE = 7.81 ANGSTROMS REMARK 525 HOH F 237 DISTANCE = 9.27 ANGSTROMS REMARK 525 HOH F 238 DISTANCE = 10.26 ANGSTROMS REMARK 525 HOH F 239 DISTANCE = 11.52 ANGSTROMS REMARK 525 HOH F 240 DISTANCE = 12.05 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 NA F 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH E 111 O REMARK 620 2 HOH E 136 O 92.4 REMARK 620 3 HOH F 208 O 78.0 167.3 REMARK 620 4 HOH F 218 O 90.1 85.3 86.5 REMARK 620 5 HOH F 224 O 172.0 95.2 94.9 93.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide A B 3 and RSQ B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide RSQ B 4 and G B 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide A C 3 and RSQ C 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide RSQ C 4 and G C 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide A D 3 and RSQ D 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide RSQ D 4 and G D 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide A E 3 and RSQ E 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide RSQ E 4 and G E 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide A F 3 and RSQ F 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide RSQ F 4 and G F 5 DBREF 5HN2 A 1 8 PDB 5HN2 5HN2 1 8 DBREF 5HN2 B 1 8 PDB 5HN2 5HN2 1 8 DBREF 5HN2 C 1 8 PDB 5HN2 5HN2 1 8 DBREF 5HN2 D 1 8 PDB 5HN2 5HN2 1 8 DBREF 5HN2 E 1 8 PDB 5HN2 5HN2 1 8 DBREF 5HN2 F 1 8 PDB 5HN2 5HN2 1 8 SEQRES 1 A 8 G U A RSQ G U A C SEQRES 1 B 8 G U A RSQ G U A C SEQRES 1 C 8 G U A RSQ G U A C SEQRES 1 D 8 G U A RSQ G U A C SEQRES 1 E 8 G U A RSQ G U A C SEQRES 1 F 8 G U A RSQ G U A C HET RSQ A 4 22 HET RSQ B 4 22 HET RSQ C 4 22 HET RSQ D 4 22 HET RSQ E 4 22 HET RSQ F 4 22 HET NA F 101 1 HETNAM RSQ 5-FORMYLCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM NA SODIUM ION FORMUL 1 RSQ 6(C10 H14 N3 O9 P) FORMUL 7 NA NA 1+ FORMUL 8 HOH *195(H2 O) LINK O3' A A 3 P RSQ A 4 1555 1555 1.62 LINK O3' RSQ A 4 P G A 5 1555 1555 1.58 LINK O3' A B 3 P RSQ B 4 1555 1555 1.62 LINK O3' RSQ B 4 P G B 5 1555 1555 1.68 LINK O3' A C 3 P RSQ C 4 1555 1555 1.51 LINK O3' RSQ C 4 P G C 5 1555 1555 1.70 LINK O3' A D 3 P RSQ D 4 1555 1555 1.62 LINK O3' RSQ D 4 P G D 5 1555 1555 1.64 LINK O3' A E 3 P RSQ E 4 1555 1555 1.66 LINK O3' RSQ E 4 P G E 5 1555 1555 1.57 LINK O3' A F 3 P RSQ F 4 1555 1555 1.65 LINK O3' RSQ F 4 P G F 5 1555 1555 1.62 LINK O HOH E 111 NA NA F 101 1555 1555 2.07 LINK O HOH E 136 NA NA F 101 1555 1555 2.16 LINK NA NA F 101 O HOH F 208 1555 1555 2.06 LINK NA NA F 101 O HOH F 218 1555 1555 2.16 LINK NA NA F 101 O HOH F 224 1555 1555 1.97 SITE 1 AC1 5 HOH E 111 HOH E 136 HOH F 208 HOH F 218 SITE 2 AC1 5 HOH F 224 SITE 1 AC2 21 G A 5 U A 6 A A 7 HOH A 107 SITE 2 AC2 21 U B 2 G B 5 HOH B 101 HOH B 103 SITE 3 AC2 21 HOH B 107 HOH B 108 HOH B 110 HOH B 111 SITE 4 AC2 21 HOH B 113 HOH B 114 HOH B 117 HOH B 119 SITE 5 AC2 21 A D 3 RSQ D 4 HOH D 101 RSQ F 4 SITE 6 AC2 21 HOH F 216 SITE 1 AC3 17 RSQ A 4 G A 5 HOH A 107 A B 3 SITE 2 AC3 17 U B 6 HOH B 102 HOH B 103 HOH B 109 SITE 3 AC3 17 HOH B 110 HOH B 114 HOH B 117 HOH B 119 SITE 4 AC3 17 A D 3 RSQ D 4 HOH D 101 HOH E 142 SITE 5 AC3 17 RSQ F 4 SITE 1 AC4 10 HOH A 130 HOH A 131 U C 2 G C 5 SITE 2 AC4 10 HOH C 108 HOH C 116 G D 5 U D 6 SITE 3 AC4 10 A D 7 HOH F 237 SITE 1 AC5 13 A C 3 U C 6 HOH C 102 HOH C 106 SITE 2 AC5 13 HOH C 108 HOH C 109 HOH C 113 HOH C 116 SITE 3 AC5 13 A D 3 RSQ D 4 G D 5 HOH E 149 SITE 4 AC5 13 HOH F 237 SITE 1 AC6 18 RSQ B 4 HOH B 110 G C 5 U C 6 SITE 2 AC6 18 A C 7 U D 2 G D 5 HOH D 101 SITE 3 AC6 18 HOH D 102 HOH D 103 HOH D 104 HOH D 109 SITE 4 AC6 18 HOH D 112 HOH D 115 HOH D 116 A F 3 SITE 5 AC6 18 RSQ F 4 HOH F 216 SITE 1 AC7 18 RSQ B 4 HOH B 110 A C 3 RSQ C 4 SITE 2 AC7 18 G C 5 U C 6 A D 3 U D 6 SITE 3 AC7 18 HOH D 102 HOH D 106 HOH D 109 HOH D 110 SITE 4 AC7 18 HOH D 114 HOH D 116 HOH E 127 A F 3 SITE 5 AC7 18 RSQ F 4 HOH F 240 SITE 1 AC8 15 U E 2 G E 5 HOH E 103 HOH E 105 SITE 2 AC8 15 HOH E 107 HOH E 108 HOH E 118 HOH E 120 SITE 3 AC8 15 HOH E 122 HOH E 125 HOH E 129 G F 5 SITE 4 AC8 15 U F 6 A F 7 HOH F 225 SITE 1 AC9 17 A E 3 U E 6 HOH E 101 HOH E 103 SITE 2 AC9 17 HOH E 105 HOH E 108 HOH E 116 HOH E 118 SITE 3 AC9 17 HOH E 121 HOH E 122 HOH E 131 HOH E 132 SITE 4 AC9 17 A F 3 RSQ F 4 G F 5 U F 6 SITE 5 AC9 17 HOH F 225 SITE 1 AD1 21 A B 3 RSQ B 4 HOH B 101 HOH B 110 SITE 2 AD1 21 HOH B 114 RSQ D 4 HOH D 102 G E 5 SITE 3 AD1 21 U E 6 A E 7 U F 2 G F 5 SITE 4 AD1 21 HOH F 202 HOH F 207 HOH F 209 HOH F 214 SITE 5 AD1 21 HOH F 215 HOH F 216 HOH F 217 HOH F 220 SITE 6 AD1 21 HOH F 223 SITE 1 AD2 20 A B 3 RSQ B 4 HOH B 101 HOH B 110 SITE 2 AD2 20 HOH B 114 RSQ D 4 A E 3 RSQ E 4 SITE 3 AD2 20 G E 5 A F 3 U F 6 HOH F 202 SITE 4 AD2 20 HOH F 204 HOH F 210 HOH F 214 HOH F 219 SITE 5 AD2 20 HOH F 220 HOH F 221 HOH F 223 HOH F 228 CRYST1 42.336 42.336 58.646 90.00 90.00 120.00 P 32 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 0.023621 0.013637 0.000000 0.00000 SCALE2 0.000000 0.027275 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017051 0.00000