HEADER TRANSFERASE 30-SEP-21 7SED TITLE CRYSTAL STRUCTURE OF HUMAN FIBRILLARIN IN COMPLEX WITH COMPOUND 2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RRNA 2'-O-METHYLTRANSFERASE FIBRILLARIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 34 KDA NUCLEOLAR SCLERODERMA ANTIGEN,HISTONE-GLUTAMINE COMPND 5 METHYLTRANSFERASE,U6 SNRNA 2'-O-METHYLTRANSFERASE FIBRILLARIN; COMPND 6 EC: 2.1.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FBL, FIB1, FLRN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYLTRANSFERASE, S-ADENOSYL METHIONINE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHI,I.M.EL-DEEB,V.MASIC,L.HARTLEY-TASSELL,A.MAGGIONI,M.VON AUTHOR 2 ITZSTEIN,T.VE REVDAT 2 18-OCT-23 7SED 1 REMARK REVDAT 1 09-FEB-22 7SED 0 JRNL AUTH Y.SHI,I.M.EL-DEEB,V.MASIC,L.HARTLEY-TASSELL,A.MAGGIONI, JRNL AUTH 2 M.V.ITZSTEIN,T.VE JRNL TITL DISCOVERY OF COFACTOR COMPETITIVE INHIBITORS AGAINST THE JRNL TITL 2 HUMAN METHYLTRANSFERASE FIBRILLARIN. JRNL REF PHARMACEUTICALS V. 15 2021 JRNL REFN ESSN 1424-8247 JRNL PMID 35056083 JRNL DOI 10.3390/PH15010026 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 38.6300 - 4.5700 1.00 1810 154 0.1690 0.2082 REMARK 3 2 4.5700 - 3.6300 1.00 1744 147 0.1526 0.1848 REMARK 3 3 3.6300 - 3.1700 1.00 1715 144 0.1862 0.2364 REMARK 3 4 3.1700 - 2.8800 1.00 1692 144 0.2237 0.2587 REMARK 3 5 2.8800 - 2.6700 1.00 1705 143 0.2099 0.2188 REMARK 3 6 2.6700 - 2.5200 1.00 1691 144 0.2093 0.2396 REMARK 3 7 2.5200 - 2.3900 1.00 1690 143 0.2091 0.2709 REMARK 3 8 2.3900 - 2.2900 0.99 1652 140 0.1992 0.2434 REMARK 3 9 2.2900 - 2.2000 1.00 1696 143 0.2013 0.2166 REMARK 3 10 2.2000 - 2.1200 0.99 1667 141 0.1909 0.2387 REMARK 3 11 2.1200 - 2.0600 0.99 1660 140 0.1859 0.2196 REMARK 3 12 2.0600 - 2.0000 0.99 1658 141 0.2009 0.2189 REMARK 3 13 2.0000 - 1.9500 0.99 1665 140 0.2307 0.2755 REMARK 3 14 1.9400 - 1.9000 0.96 1612 136 0.2914 0.3040 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.219 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.56 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 : 0.011 1827 REMARK 3 ANGLE : 1.105 2477 REMARK 3 CHIRALITY : 0.071 280 REMARK 3 PLANARITY : 0.008 328 REMARK 3 DIHEDRAL : 13.196 687 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7SED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1000258904. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-19 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: 2IPX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.75-3.3 M SODIUM FORMATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.12450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.12450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 34.64550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.79050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.64550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.79050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.12450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.64550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.79050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.12450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.64550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.79050 REMARK 290 SMTRY3 8 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 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 SER A 80 REMARK 465 ASN A 81 REMARK 465 ALA A 82 REMARK 465 GLY A 83 REMARK 465 LYS A 84 REMARK 465 ASN A 85 REMARK 465 ARG A 100 REMARK 465 GLY A 101 REMARK 465 LYS A 102 REMARK 465 GLU A 103 REMARK 465 ASP A 104 REMARK 465 LYS A 318 REMARK 465 VAL A 319 REMARK 465 LYS A 320 REMARK 465 ASN A 321 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 HIS A 156 -24.04 68.20 REMARK 500 ALA A 169 -134.93 49.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 7SED A 83 321 UNP P22087 FBRL_HUMAN 83 321 SEQADV 7SED SER A 80 UNP P22087 EXPRESSION TAG SEQADV 7SED ASN A 81 UNP P22087 EXPRESSION TAG SEQADV 7SED ALA A 82 UNP P22087 EXPRESSION TAG SEQRES 1 A 242 SER ASN ALA GLY LYS ASN VAL MET VAL GLU PRO HIS ARG SEQRES 2 A 242 HIS GLU GLY VAL PHE ILE CYS ARG GLY LYS GLU ASP ALA SEQRES 3 A 242 LEU VAL THR LYS ASN LEU VAL PRO GLY GLU SER VAL TYR SEQRES 4 A 242 GLY GLU LYS ARG VAL SER ILE SER GLU GLY ASP ASP LYS SEQRES 5 A 242 ILE GLU TYR ARG ALA TRP ASN PRO PHE ARG SER LYS LEU SEQRES 6 A 242 ALA ALA ALA ILE LEU GLY GLY VAL ASP GLN ILE HIS ILE SEQRES 7 A 242 LYS PRO GLY ALA LYS VAL LEU TYR LEU GLY ALA ALA SER SEQRES 8 A 242 GLY THR THR VAL SER HIS VAL SER ASP ILE VAL GLY PRO SEQRES 9 A 242 ASP GLY LEU VAL TYR ALA VAL GLU PHE SER HIS ARG SER SEQRES 10 A 242 GLY ARG ASP LEU ILE ASN LEU ALA LYS LYS ARG THR ASN SEQRES 11 A 242 ILE ILE PRO VAL ILE GLU ASP ALA ARG HIS PRO HIS LYS SEQRES 12 A 242 TYR ARG MET LEU ILE ALA MET VAL ASP VAL ILE PHE ALA SEQRES 13 A 242 ASP VAL ALA GLN PRO ASP GLN THR ARG ILE VAL ALA LEU SEQRES 14 A 242 ASN ALA HIS THR PHE LEU ARG ASN GLY GLY HIS PHE VAL SEQRES 15 A 242 ILE SER ILE LYS ALA ASN CYS ILE ASP SER THR ALA SER SEQRES 16 A 242 ALA GLU ALA VAL PHE ALA SER GLU VAL LYS LYS MET GLN SEQRES 17 A 242 GLN GLU ASN MET LYS PRO GLN GLU GLN LEU THR LEU GLU SEQRES 18 A 242 PRO TYR GLU ARG ASP HIS ALA VAL VAL VAL GLY VAL TYR SEQRES 19 A 242 ARG PRO PRO PRO LYS VAL LYS ASN HET 8VD A 401 30 HET FMT A 402 5 HETNAM 8VD N-(PIPERIDIN-4-YL)-6-(TRIFLUOROMETHYL)PYRIMIDIN-4-AMINE HETNAM FMT FORMIC ACID FORMUL 2 8VD C10 H13 F3 N4 FORMUL 3 FMT C H2 O2 FORMUL 4 HOH *89(H2 O) HELIX 1 AA1 SER A 142 GLY A 150 1 9 HELIX 2 AA2 GLY A 171 GLY A 182 1 12 HELIX 3 AA3 SER A 193 ARG A 207 1 15 HELIX 4 AA4 HIS A 219 ILE A 227 5 9 HELIX 5 AA5 ASP A 241 PHE A 253 1 13 HELIX 6 AA6 ALA A 266 ASP A 270 1 5 HELIX 7 AA7 SER A 274 GLN A 288 1 15 SHEET 1 AA1 5 GLU A 89 PRO A 90 0 SHEET 2 AA1 5 VAL A 96 ILE A 98 -1 O ILE A 98 N GLU A 89 SHEET 3 AA1 5 VAL A 107 LYS A 109 -1 O VAL A 107 N PHE A 97 SHEET 4 AA1 5 ASP A 130 ALA A 136 -1 O ARG A 135 N THR A 108 SHEET 5 AA1 5 ARG A 122 GLU A 127 -1 N ILE A 125 O ILE A 132 SHEET 1 AA2 7 ILE A 210 VAL A 213 0 SHEET 2 AA2 7 LEU A 186 VAL A 190 1 N ALA A 189 O ILE A 211 SHEET 3 AA2 7 LYS A 162 LEU A 166 1 N TYR A 165 O TYR A 188 SHEET 4 AA2 7 VAL A 230 ALA A 235 1 O PHE A 234 N LEU A 166 SHEET 5 AA2 7 LEU A 254 LYS A 265 1 O SER A 263 N ALA A 235 SHEET 6 AA2 7 HIS A 306 TYR A 313 -1 O ALA A 307 N ILE A 264 SHEET 7 AA2 7 MET A 291 THR A 298 -1 N GLN A 294 O VAL A 310 CISPEP 1 GLU A 300 PRO A 301 0 2.00 CRYST1 69.291 139.581 66.249 90.00 90.00 90.00 C 2 2 21 8 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 0.014432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007164 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015095 0.00000