HEADER RNA 18-JAN-23 8I3Z TITLE CRYSTAL STRUCTURE OF NAD-II RIBOSWITCH (TWO STRANDS) WITH NMN AT 1.67 TITLE 2 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV) COMPND 4 P*GP*CP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (31-MER); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PARASANGUINIS; SOURCE 4 ORGANISM_TAXID: 1318; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PARASANGUINIS; SOURCE 8 ORGANISM_TAXID: 1318 KEYWDS APTAMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR X.PENG,D.M.J.LILLEY,L.HUANG REVDAT 3 29-MAY-24 8I3Z 1 REMARK REVDAT 2 19-APR-23 8I3Z 1 JRNL REVDAT 1 22-MAR-23 8I3Z 0 JRNL AUTH X.PENG,W.LIAO,X.LIN,D.M.J.LILLEY,L.HUANG JRNL TITL CRYSTAL STRUCTURES OF THE NAD+-II RIBOSWITCH REVEAL TWO JRNL TITL 2 DISTINCT LIGAND-BINDING POCKETS. JRNL REF NUCLEIC ACIDS RES. V. 51 2904 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36840714 JRNL DOI 10.1093/NAR/GKAD102 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4788 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 27460 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.5900 - 3.6000 1.00 2759 156 0.1266 0.1258 REMARK 3 2 3.6000 - 2.8600 1.00 2681 117 0.1513 0.2245 REMARK 3 3 2.8500 - 2.4900 1.00 2654 140 0.2100 0.2262 REMARK 3 4 2.4900 - 2.2700 1.00 2587 164 0.2103 0.2103 REMARK 3 5 2.2700 - 2.1000 1.00 2628 139 0.2018 0.1982 REMARK 3 6 2.1000 - 1.9800 1.00 2638 110 0.2074 0.2314 REMARK 3 7 1.9800 - 1.8800 1.00 2563 154 0.2069 0.2246 REMARK 3 8 1.8800 - 1.8000 1.00 2629 134 0.2226 0.2344 REMARK 3 9 1.8000 - 1.7300 0.98 2531 126 0.2255 0.2585 REMARK 3 10 1.7300 - 1.6700 0.93 2421 129 0.2319 0.2753 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.172 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.994 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.31 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 1366 REMARK 3 ANGLE : 1.890 2124 REMARK 3 CHIRALITY : 0.085 280 REMARK 3 PLANARITY : 0.021 59 REMARK 3 DIHEDRAL : 17.044 662 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4154 30.4367 7.5622 REMARK 3 T TENSOR REMARK 3 T11: 0.2188 T22: 0.3666 REMARK 3 T33: 0.4180 T12: -0.0135 REMARK 3 T13: 0.0045 T23: 0.0759 REMARK 3 L TENSOR REMARK 3 L11: 0.3674 L22: 1.3047 REMARK 3 L33: 1.9230 L12: -0.1270 REMARK 3 L13: -0.7402 L23: -0.9101 REMARK 3 S TENSOR REMARK 3 S11: -0.1179 S12: -0.0855 S13: -0.2522 REMARK 3 S21: -0.1359 S22: -0.0220 S23: -0.2004 REMARK 3 S31: 0.2408 S32: -0.4954 S33: 0.1193 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2485 34.5114 17.2613 REMARK 3 T TENSOR REMARK 3 T11: 0.1896 T22: 0.3147 REMARK 3 T33: 0.3500 T12: -0.0428 REMARK 3 T13: 0.0089 T23: 0.0368 REMARK 3 L TENSOR REMARK 3 L11: 6.7864 L22: 2.8710 REMARK 3 L33: 2.1040 L12: -1.3798 REMARK 3 L13: -1.3077 L23: -0.8634 REMARK 3 S TENSOR REMARK 3 S11: -0.0165 S12: 0.1759 S13: 0.6154 REMARK 3 S21: -0.0153 S22: 0.0149 S23: -0.3872 REMARK 3 S31: -0.0830 S32: 0.2038 S33: 0.0028 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.1365 23.8774 6.5321 REMARK 3 T TENSOR REMARK 3 T11: 0.3121 T22: 0.5828 REMARK 3 T33: 0.3081 T12: 0.0284 REMARK 3 T13: -0.0416 T23: -0.1055 REMARK 3 L TENSOR REMARK 3 L11: 1.7270 L22: 2.4803 REMARK 3 L33: 6.6481 L12: 1.6290 REMARK 3 L13: -0.6135 L23: 0.1105 REMARK 3 S TENSOR REMARK 3 S11: -0.0994 S12: 0.9142 S13: -0.4769 REMARK 3 S21: -0.5253 S22: 0.0316 S23: 0.0209 REMARK 3 S31: 0.4168 S32: 0.0635 S33: 0.0384 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 24 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.0741 14.3227 -16.2034 REMARK 3 T TENSOR REMARK 3 T11: 1.3049 T22: 1.9787 REMARK 3 T33: 0.7967 T12: 0.2088 REMARK 3 T13: -0.0724 T23: -0.6338 REMARK 3 L TENSOR REMARK 3 L11: 7.6977 L22: 7.9455 REMARK 3 L33: 0.5447 L12: 2.4871 REMARK 3 L13: -0.3057 L23: -1.4741 REMARK 3 S TENSOR REMARK 3 S11: -0.2302 S12: -0.1296 S13: -0.4923 REMARK 3 S21: -1.4071 S22: 0.0342 S23: -0.4133 REMARK 3 S31: 0.5855 S32: 1.3966 S33: 0.1127 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 27 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4471 30.0518 4.2140 REMARK 3 T TENSOR REMARK 3 T11: 0.3084 T22: 0.7104 REMARK 3 T33: 0.4829 T12: -0.0238 REMARK 3 T13: 0.0324 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 7.2091 L22: 0.7292 REMARK 3 L33: 3.9018 L12: 0.0941 REMARK 3 L13: 2.5704 L23: 0.1843 REMARK 3 S TENSOR REMARK 3 S11: 0.3516 S12: 1.2273 S13: -0.7223 REMARK 3 S21: -0.1410 S22: 0.0666 S23: -0.4081 REMARK 3 S31: 0.4832 S32: 0.0766 S33: -0.4066 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 37 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.9610 29.0965 12.1382 REMARK 3 T TENSOR REMARK 3 T11: 0.2489 T22: 0.4163 REMARK 3 T33: 0.4959 T12: 0.0422 REMARK 3 T13: -0.0054 T23: 0.1354 REMARK 3 L TENSOR REMARK 3 L11: 4.0473 L22: 0.2109 REMARK 3 L33: 3.3695 L12: 0.8089 REMARK 3 L13: -0.4890 L23: -0.0695 REMARK 3 S TENSOR REMARK 3 S11: -0.1540 S12: -0.4391 S13: -0.1847 REMARK 3 S21: 0.0737 S22: 0.2008 S23: -0.2738 REMARK 3 S31: 0.3576 S32: 0.3366 S33: -0.0319 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 42 THROUGH 51 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.7023 35.8045 15.8532 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.3350 REMARK 3 T33: 0.3604 T12: -0.0776 REMARK 3 T13: 0.0051 T23: 0.1202 REMARK 3 L TENSOR REMARK 3 L11: 7.1619 L22: 2.3096 REMARK 3 L33: 1.9498 L12: -0.5574 REMARK 3 L13: -0.7948 L23: 0.7333 REMARK 3 S TENSOR REMARK 3 S11: -0.0324 S12: -0.1795 S13: 0.7887 REMARK 3 S21: 0.0814 S22: -0.0716 S23: -0.2768 REMARK 3 S31: -0.0133 S32: 0.1037 S33: 0.1911 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 52 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2657 28.2853 11.6855 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.4338 REMARK 3 T33: 0.2558 T12: -0.0463 REMARK 3 T13: -0.0268 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 2.1560 L22: 5.5309 REMARK 3 L33: 2.6975 L12: 0.9992 REMARK 3 L13: 1.3278 L23: -0.1315 REMARK 3 S TENSOR REMARK 3 S11: 0.0269 S12: 0.6877 S13: 0.1011 REMARK 3 S21: 0.0518 S22: -0.0369 S23: 0.5158 REMARK 3 S31: 0.3296 S32: -0.4505 S33: 0.0561 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8I3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27501 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 46.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 16.00 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.96200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: 8HB1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, HANGING 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 41.23667 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 20.61833 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 20.61833 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 41.23667 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: 4660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 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 228 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 233 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 257 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 HO3' CBV A 21 P G A 22 0.69 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 P A A 3 O5' -0.072 REMARK 500 A A 3 O5' A A 3 C5' -0.080 REMARK 500 C A 10 N1 C A 10 C6 -0.038 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 1 N1 - C2 - N3 ANGL. DEV. = 3.1 DEGREES REMARK 500 A A 1 C2 - N3 - C4 ANGL. DEV. = -5.4 DEGREES REMARK 500 A A 1 C5 - C6 - N1 ANGL. DEV. = -3.4 DEGREES REMARK 500 A A 3 O5' - P - OP1 ANGL. DEV. = -13.0 DEGREES REMARK 500 A A 3 O5' - P - OP2 ANGL. DEV. = 8.3 DEGREES REMARK 500 A A 3 C5' - C4' - C3' ANGL. DEV. = -10.8 DEGREES REMARK 500 A A 3 C2 - N3 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 A A 3 C5 - N7 - C8 ANGL. DEV. = -3.6 DEGREES REMARK 500 U A 7 C5 - C6 - N1 ANGL. DEV. = -3.2 DEGREES REMARK 500 G A 11 O5' - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 G A 11 C2 - N3 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 G A 11 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 G A 11 C5 - C6 - O6 ANGL. DEV. = 5.7 DEGREES REMARK 500 C B 46 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 A B 47 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 A B 50 N1 - C2 - N3 ANGL. DEV. = -3.8 DEGREES REMARK 500 G B 52 C2 - N3 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 G B 52 N3 - C4 - C5 ANGL. DEV. = 3.1 DEGREES REMARK 500 A B 55 O5' - P - OP2 ANGL. DEV. = -5.7 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 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 15 OP1 REMARK 620 2 A A 16 OP1 99.7 REMARK 620 N 1 DBREF 8I3Z A 1 24 PDB 8I3Z 8I3Z 1 24 DBREF 8I3Z B 26 56 PDB 8I3Z 8I3Z 26 56 SEQRES 1 A 24 A G A G C G U U G C G U C SEQRES 2 A 24 C G A A A G U CBV G C C SEQRES 1 B 31 G C G A C A C G G C U C U SEQRES 2 B 31 U U A A A A A C A A A A G SEQRES 3 B 31 G A G A A HET CBV A 21 32 HET NA A 101 1 HET NMN B 101 36 HET NMN B 102 36 HET NA B 103 1 HET NA B 104 1 HET NA B 105 1 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM NA SODIUM ION HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE FORMUL 1 CBV C9 H13 BR N3 O8 P FORMUL 3 NA 4(NA 1+) FORMUL 4 NMN 2(C11 H16 N2 O8 P 1+) FORMUL 9 HOH *146(H2 O) LINK O3' U A 20 P CBV A 21 1555 1555 1.61 LINK O3' CBV A 21 P G A 22 1555 1555 1.59 LINK OP1 G A 15 NA NA A 101 1555 1555 2.83 LINK OP1 A A 16 NA NA A 101 1555 1555 2.91 LINK OP2 A B 56 NA NA B 105 1555 5565 2.74 CRYST1 81.271 81.271 61.855 90.00 90.00 120.00 P 32 2 1 6 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 0.012305 0.007104 0.000000 0.00000 SCALE2 0.000000 0.014208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016167 0.00000