HEADER TRANSFERASE 15-NOV-18 6IRZ TITLE CRYSTAL STRUCTURE OF THE ZEBRAFISH CAP-SPECIFIC ADENOSINE TITLE 2 METHYLTRANSFERASE BOUND TO SAH AND M7G-CAPPED RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PDX1 C-TERMINAL-INHIBITING FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: PCIF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PE-SUMO KEYWDS RNA METHYLATION, METHYLTRANSFERASE, M6A, N6-METHYLADENOSINE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.HIRANO,H.NISHIMASU,R.ISHITANI,O.NUREKI REVDAT 4 22-NOV-23 6IRZ 1 REMARK REVDAT 3 28-OCT-20 6IRZ 1 JRNL REVDAT 2 23-JAN-19 6IRZ 1 JRNL REVDAT 1 05-DEC-18 6IRZ 0 JRNL AUTH S.AKICHIKA,S.HIRANO,Y.SHICHINO,T.SUZUKI,H.NISHIMASU, JRNL AUTH 2 R.ISHITANI,A.SUGITA,Y.HIROSE,S.IWASAKI,O.NUREKI,T.SUZUKI JRNL TITL CAP-SPECIFIC TERMINAL N 6 -METHYLATION OF RNA BY AN RNA JRNL TITL 2 POLYMERASE II-ASSOCIATED METHYLTRANSFERASE. JRNL REF SCIENCE V. 363 2019 JRNL REFN ESSN 1095-9203 JRNL PMID 30467178 JRNL DOI 10.1126/SCIENCE.AAV0080 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38058 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1884 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 46.5786 - 4.7013 1.00 2971 167 0.1534 0.1539 REMARK 3 2 4.7013 - 3.7321 1.00 2847 153 0.1467 0.1786 REMARK 3 3 3.7321 - 3.2604 1.00 2844 119 0.1791 0.2184 REMARK 3 4 3.2604 - 2.9624 1.00 2799 140 0.1988 0.2355 REMARK 3 5 2.9624 - 2.7501 1.00 2779 169 0.2033 0.2577 REMARK 3 6 2.7501 - 2.5880 1.00 2804 126 0.1921 0.2012 REMARK 3 7 2.5880 - 2.4584 1.00 2741 179 0.1935 0.2373 REMARK 3 8 2.4584 - 2.3514 1.00 2774 140 0.1946 0.2293 REMARK 3 9 2.3514 - 2.2608 0.98 2720 124 0.2065 0.2382 REMARK 3 10 2.2608 - 2.1828 0.97 2657 159 0.2584 0.3254 REMARK 3 11 2.1828 - 2.1146 1.00 2759 132 0.2142 0.2446 REMARK 3 12 2.1146 - 2.0541 0.98 2747 134 0.2786 0.3392 REMARK 3 13 2.0541 - 2.0001 1.00 2732 142 0.2525 0.3022 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.64 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 178 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.1105 8.1985 19.0965 REMARK 3 T TENSOR REMARK 3 T11: 0.2538 T22: 0.2966 REMARK 3 T33: 0.2589 T12: 0.0212 REMARK 3 T13: -0.0261 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 1.4611 L22: 1.0558 REMARK 3 L33: 2.3533 L12: -0.2898 REMARK 3 L13: -0.3748 L23: -0.2131 REMARK 3 S TENSOR REMARK 3 S11: -0.0436 S12: -0.0498 S13: 0.0950 REMARK 3 S21: 0.1307 S22: 0.0414 S23: -0.0050 REMARK 3 S31: -0.0396 S32: -0.0026 S33: -0.0090 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 334 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5658 16.5632 33.6505 REMARK 3 T TENSOR REMARK 3 T11: 0.4578 T22: 0.5902 REMARK 3 T33: 0.5005 T12: 0.1332 REMARK 3 T13: 0.0013 T23: -0.0318 REMARK 3 L TENSOR REMARK 3 L11: 2.1638 L22: 2.4976 REMARK 3 L33: 2.1427 L12: -1.0228 REMARK 3 L13: 0.3783 L23: -1.0129 REMARK 3 S TENSOR REMARK 3 S11: -0.3262 S12: -0.3230 S13: 0.0095 REMARK 3 S21: -0.0025 S22: 0.0936 S23: 0.3272 REMARK 3 S31: 0.0969 S32: -0.4672 S33: 0.2731 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 335 THROUGH 389 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.7743 8.7420 28.7235 REMARK 3 T TENSOR REMARK 3 T11: 0.3995 T22: 0.3100 REMARK 3 T33: 0.2799 T12: 0.0213 REMARK 3 T13: -0.0426 T23: 0.0258 REMARK 3 L TENSOR REMARK 3 L11: 1.5167 L22: 0.2509 REMARK 3 L33: 1.9350 L12: -0.0057 REMARK 3 L13: -0.6850 L23: 0.5585 REMARK 3 S TENSOR REMARK 3 S11: -0.0843 S12: -0.4048 S13: -0.0291 REMARK 3 S21: -0.0706 S22: 0.0607 S23: 0.0744 REMARK 3 S31: -0.0707 S32: 0.1272 S33: 0.0845 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 390 THROUGH 423 ) REMARK 3 ORIGIN FOR THE GROUP (A): 72.6917 5.4730 8.7146 REMARK 3 T TENSOR REMARK 3 T11: 0.3079 T22: 0.5370 REMARK 3 T33: 0.3728 T12: 0.0810 REMARK 3 T13: -0.0444 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.4899 L22: 4.1823 REMARK 3 L33: 1.7586 L12: 0.5038 REMARK 3 L13: -0.5248 L23: -0.4462 REMARK 3 S TENSOR REMARK 3 S11: -0.1497 S12: -0.0221 S13: 0.0549 REMARK 3 S21: 0.0499 S22: 0.0305 S23: -0.1670 REMARK 3 S31: 0.0617 S32: 0.5922 S33: 0.0501 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 424 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.3191 0.9123 -3.5960 REMARK 3 T TENSOR REMARK 3 T11: 0.4199 T22: 0.5251 REMARK 3 T33: 0.3168 T12: 0.0072 REMARK 3 T13: -0.0277 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 2.2596 L22: 2.6367 REMARK 3 L33: 2.3387 L12: -0.2159 REMARK 3 L13: 0.4239 L23: 0.0925 REMARK 3 S TENSOR REMARK 3 S11: 0.0672 S12: 0.6293 S13: -0.1908 REMARK 3 S21: -0.3087 S22: -0.0491 S23: 0.2138 REMARK 3 S31: 0.3508 S32: -0.2463 S33: -0.0009 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 460 THROUGH 532 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.0645 13.0859 3.3039 REMARK 3 T TENSOR REMARK 3 T11: 0.2596 T22: 0.3575 REMARK 3 T33: 0.3197 T12: 0.0177 REMARK 3 T13: -0.0342 T23: 0.0297 REMARK 3 L TENSOR REMARK 3 L11: 1.2547 L22: 2.8807 REMARK 3 L33: 1.5356 L12: -0.0347 REMARK 3 L13: -0.0857 L23: 0.1661 REMARK 3 S TENSOR REMARK 3 S11: -0.0831 S12: 0.1630 S13: 0.2684 REMARK 3 S21: -0.0312 S22: 0.1111 S23: 0.1249 REMARK 3 S31: -0.1007 S32: -0.0241 S33: -0.0189 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 533 THROUGH 616 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.2574 26.5809 14.9429 REMARK 3 T TENSOR REMARK 3 T11: 0.4759 T22: 0.2979 REMARK 3 T33: 0.4691 T12: -0.0098 REMARK 3 T13: -0.0239 T23: -0.0223 REMARK 3 L TENSOR REMARK 3 L11: 2.5204 L22: 1.9249 REMARK 3 L33: 2.9242 L12: 0.1433 REMARK 3 L13: -0.6228 L23: 0.1635 REMARK 3 S TENSOR REMARK 3 S11: 0.0401 S12: -0.1611 S13: 0.6304 REMARK 3 S21: 0.4266 S22: 0.0393 S23: 0.0325 REMARK 3 S31: -0.6168 S32: 0.2281 S33: -0.0343 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 617 THROUGH 673 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.0811 33.3807 4.3976 REMARK 3 T TENSOR REMARK 3 T11: 0.6819 T22: 0.3945 REMARK 3 T33: 0.8387 T12: 0.0462 REMARK 3 T13: -0.0636 T23: 0.1423 REMARK 3 L TENSOR REMARK 3 L11: 1.6466 L22: 1.7050 REMARK 3 L33: 3.1074 L12: -1.1458 REMARK 3 L13: -0.1319 L23: 0.1844 REMARK 3 S TENSOR REMARK 3 S11: 0.2397 S12: 0.1899 S13: 0.6649 REMARK 3 S21: 0.0760 S22: -0.2351 S23: 0.1935 REMARK 3 S31: -0.6364 S32: -0.4179 S33: -0.0405 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 6IRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38329 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.65400 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: MOLREP REMARK 200 STARTING MODEL: 6IRX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 3350, 0.1M POTASSIUM REMARK 280 THIOCYANATE, 0.1M BIS-TRIS PROPANE, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 35.83450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.56600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.58250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.56600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.83450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.58250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 GLY A 396 REMARK 465 THR A 397 REMARK 465 GLU A 398 REMARK 465 SER A 399 REMARK 465 ALA A 400 REMARK 465 GLU A 401 REMARK 465 GLY A 487 REMARK 465 VAL A 488 REMARK 465 ASN A 489 REMARK 465 GLU A 490 REMARK 465 GLY A 491 REMARK 465 SER A 492 REMARK 465 SER A 625 REMARK 465 GLY A 626 REMARK 465 SER A 627 REMARK 465 GLN A 628 REMARK 465 HIS A 629 REMARK 465 ILE A 630 REMARK 465 CYS A 631 REMARK 465 LYS A 632 REMARK 465 ARG A 633 REMARK 465 GLU A 634 REMARK 465 GLU A 635 REMARK 465 ILE A 636 REMARK 465 TYR A 637 REMARK 465 TYR A 638 REMARK 465 LYS A 639 REMARK 465 ALA A 640 REMARK 465 ILE A 641 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 281 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 331 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 673 CG CD CE NZ 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 ARG A 193 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 193 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 257 -10.21 -155.29 REMARK 500 GLU A 258 80.51 -150.79 REMARK 500 ASP A 404 32.66 -98.64 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 960 DISTANCE = 5.84 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue M7G A 705 DBREF1 6IRZ A 178 673 UNP A0A0R4IKJ1_DANRE DBREF2 6IRZ A A0A0R4IKJ1 178 673 SEQADV 6IRZ VAL A 308 UNP A0A0R4IKJ ALA 308 ENGINEERED MUTATION SEQADV 6IRZ ASN A 344 UNP A0A0R4IKJ HIS 344 ENGINEERED MUTATION SEQRES 1 A 496 VAL TYR TRP ASP LEU ASP ILE GLN THR ASN ALA VAL ILE SEQRES 2 A 496 ARG GLU ARG ALA PRO ALA ASP HIS LEU PRO PRO HIS PRO SEQRES 3 A 496 GLU ILE GLU LEU GLN ARG ALA GLN LEU THR THR LYS LEU SEQRES 4 A 496 ARG GLN HIS TYR HIS GLU LEU CYS SER GLN ARG GLU GLY SEQRES 5 A 496 ILE GLU PRO PRO ARG GLU SER PHE ASN ARG TRP LEU LEU SEQRES 6 A 496 GLU ARG LYS VAL VAL ASP LYS GLY LEU ASP PRO LEU LEU SEQRES 7 A 496 PRO SER GLU CYS ASP PRO VAL ILE SER PRO SER MET PHE SEQRES 8 A 496 ARG GLU ILE MET ASN ASP ILE PRO ILE ARG LEU SER ARG SEQRES 9 A 496 ILE LYS TYR LYS GLU GLU ALA ARG LYS LEU LEU PHE LYS SEQRES 10 A 496 TYR ALA GLU ALA ALA LYS LYS MET ILE ASP SER ARG ASN SEQRES 11 A 496 VAL THR PRO GLU SER ARG LYS VAL VAL LYS TRP ASN VAL SEQRES 12 A 496 GLU ASP THR MET ASN TRP LEU ARG ARG ASP HIS SER ALA SEQRES 13 A 496 SER LYS GLU ASP TYR MET ASP ARG LEU GLU ASN LEU ARG SEQRES 14 A 496 LYS GLN CYS GLY PRO HIS VAL ALA SER VAL ALA LYS ASP SEQRES 15 A 496 SER VAL GLU GLY ILE CYS SER LYS ILE TYR HIS ILE SER SEQRES 16 A 496 ALA GLU TYR VAL ARG ARG ILE ARG GLN ALA HIS LEU THR SEQRES 17 A 496 LEU LEU LYS GLU CYS ASN ILE SER VAL ASP GLY THR GLU SEQRES 18 A 496 SER ALA GLU VAL GLN ASP ARG LEU VAL TYR CYS TYR PRO SEQRES 19 A 496 VAL ARG LEU SER ILE PRO ALA PRO PRO GLN THR ARG VAL SEQRES 20 A 496 GLU LEU HIS PHE GLU ASN ASP ILE ALA CYS LEU ARG PHE SEQRES 21 A 496 LYS GLY GLU MET VAL LYS VAL SER ARG GLY HIS PHE ASN SEQRES 22 A 496 LYS LEU GLU LEU LEU TYR ARG TYR SER CYS ILE ASP ASP SEQRES 23 A 496 PRO ARG PHE GLU LYS PHE LEU SER ARG VAL TRP CYS LEU SEQRES 24 A 496 ILE LYS ARG TYR GLN VAL MET PHE GLY SER GLY VAL ASN SEQRES 25 A 496 GLU GLY SER GLY LEU GLN GLY SER LEU PRO VAL PRO VAL SEQRES 26 A 496 PHE GLU ALA LEU ASN LYS GLN PHE GLY VAL THR PHE GLU SEQRES 27 A 496 CYS PHE ALA SER PRO LEU ASN CYS TYR PHE LYS GLN PHE SEQRES 28 A 496 CYS SER ALA PHE PRO ASP ILE ASP GLY PHE PHE GLY SER SEQRES 29 A 496 ARG GLY PRO PHE LEU SER PHE SER PRO ALA SER GLY SER SEQRES 30 A 496 PHE GLU ALA ASN PRO PRO PHE CYS GLU GLU LEU MET ASP SEQRES 31 A 496 ALA MET VAL THR HIS PHE GLU ASP LEU LEU GLY ARG SER SEQRES 32 A 496 SER GLU PRO LEU SER PHE ILE ILE PHE VAL PRO GLU TRP SEQRES 33 A 496 ARG ASP PRO PRO THR PRO ALA LEU THR ARG MET GLU ALA SEQRES 34 A 496 SER ARG PHE ARG ARG HIS GLN MET THR VAL PRO ALA PHE SEQRES 35 A 496 GLU HIS GLU TYR ARG SER GLY SER GLN HIS ILE CYS LYS SEQRES 36 A 496 ARG GLU GLU ILE TYR TYR LYS ALA ILE HIS GLY THR ALA SEQRES 37 A 496 VAL ILE PHE LEU GLN ASN ASN ALA GLY PHE ALA LYS TRP SEQRES 38 A 496 GLU PRO THR THR GLU ARG ILE GLN GLU LEU LEU ALA ALA SEQRES 39 A 496 TYR LYS HET SAH A 701 26 HET EDO A 702 4 HET EDO A 703 4 HET EDO A 704 4 HET M7G A 705 29 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM EDO 1,2-ETHANEDIOL HETNAM M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 M7G C11 H19 N5 O11 P2 FORMUL 7 HOH *160(H2 O) HELIX 1 AA1 HIS A 202 GLY A 229 1 28 HELIX 2 AA2 GLU A 235 ASP A 248 1 14 HELIX 3 AA3 SER A 264 ASP A 274 1 11 HELIX 4 AA4 TYR A 284 ARG A 306 1 23 HELIX 5 AA5 THR A 309 ARG A 328 1 20 HELIX 6 AA6 SER A 334 CYS A 390 1 57 HELIX 7 AA7 ARG A 446 CYS A 460 1 15 HELIX 8 AA8 LYS A 468 GLY A 485 1 18 HELIX 9 AA9 PRO A 499 GLY A 511 1 13 HELIX 10 AB1 PHE A 532 GLY A 537 1 6 HELIX 11 AB2 PHE A 538 GLY A 540 5 3 HELIX 12 AB3 PRO A 544 PHE A 548 5 5 HELIX 13 AB4 CYS A 562 SER A 580 1 19 HELIX 14 AB5 THR A 598 ALA A 606 1 9 HELIX 15 AB6 ASN A 651 TRP A 658 1 8 HELIX 16 AB7 THR A 661 ALA A 671 1 11 SHEET 1 AA1 4 LEU A 406 TYR A 408 0 SHEET 2 AA1 4 VAL A 189 ARG A 191 -1 N ILE A 190 O VAL A 407 SHEET 3 AA1 4 PRO A 550 ALA A 557 -1 O ALA A 551 N VAL A 189 SHEET 4 AA1 4 PHE A 514 GLU A 515 1 N PHE A 514 O GLU A 556 SHEET 1 AA2 6 LEU A 406 TYR A 408 0 SHEET 2 AA2 6 VAL A 189 ARG A 191 -1 N ILE A 190 O VAL A 407 SHEET 3 AA2 6 PRO A 550 ALA A 557 -1 O ALA A 551 N VAL A 189 SHEET 4 AA2 6 LEU A 584 PRO A 591 1 O PHE A 589 N ALA A 557 SHEET 5 AA2 6 THR A 644 GLN A 650 -1 O ALA A 645 N VAL A 590 SHEET 6 AA2 6 ARG A 610 VAL A 616 -1 N ARG A 611 O PHE A 648 SHEET 1 AA3 3 GLU A 425 GLU A 429 0 SHEET 2 AA3 3 ILE A 432 PHE A 437 -1 O CYS A 434 N HIS A 427 SHEET 3 AA3 3 GLU A 440 SER A 445 -1 O VAL A 444 N ALA A 433 CISPEP 1 ASP A 260 PRO A 261 0 6.74 CISPEP 2 ILE A 275 PRO A 276 0 7.23 CISPEP 3 ASP A 595 PRO A 596 0 -4.15 SITE 1 AC1 22 GLN A 495 GLY A 496 LEU A 498 PHE A 503 SITE 2 AC1 22 GLU A 515 CYS A 516 PHE A 517 ALA A 518 SITE 3 AC1 22 SER A 519 ASN A 522 CYS A 529 SER A 530 SITE 4 AC1 22 ALA A 531 PHE A 545 GLU A 556 ASN A 558 SITE 5 AC1 22 PRO A 560 HOH A 804 HOH A 820 HOH A 829 SITE 6 AC1 22 HOH A 878 HOH A 909 SITE 1 AC2 6 LEU A 241 LYS A 245 PRO A 253 LEU A 254 SITE 2 AC2 6 ALA A 531 HOH A 804 SITE 1 AC3 8 PRO A 201 HIS A 202 PRO A 203 PRO A 419 SITE 2 AC3 8 PRO A 420 LYS A 468 SER A 471 HOH A 862 SITE 1 AC4 6 ARG A 413 LEU A 414 ASP A 462 PHE A 538 SITE 2 AC4 6 HOH A 807 HOH A 821 SITE 1 AC5 9 ARG A 239 ARG A 269 GLU A 563 TRP A 593 SITE 2 AC5 9 ASP A 595 PRO A 596 PRO A 597 HIS A 642 SITE 3 AC5 9 HOH A 801 CRYST1 71.669 83.165 93.132 90.00 90.00 90.00 P 21 21 21 4 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 0.013953 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010737 0.00000