HEADER TRANSFERASE 30-SEP-21 7SE7 TITLE CRYSTAL STRUCTURE OF HUMAN FIBRILLARIN IN COMPLEX WITH S-ADENOSYL-L- TITLE 2 METHIONINE 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 7SE7 1 REMARK REVDAT 1 09-FEB-22 7SE7 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 32329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 45.0800 - 4.2200 1.00 2304 152 0.1674 0.1707 REMARK 3 2 4.2200 - 3.3500 1.00 2215 145 0.1510 0.1848 REMARK 3 3 3.3500 - 2.9200 1.00 2195 145 0.1906 0.2379 REMARK 3 4 2.9200 - 2.6600 1.00 2157 142 0.1910 0.2193 REMARK 3 5 2.6600 - 2.4700 1.00 2176 144 0.1880 0.2406 REMARK 3 6 2.4700 - 2.3200 1.00 2154 141 0.1780 0.2304 REMARK 3 7 2.3200 - 2.2000 1.00 2152 143 0.1736 0.1887 REMARK 3 8 2.2000 - 2.1100 1.00 2146 141 0.1740 0.2262 REMARK 3 9 2.1100 - 2.0300 1.00 2160 142 0.1708 0.2142 REMARK 3 10 2.0300 - 1.9600 1.00 2140 142 0.1849 0.2016 REMARK 3 11 1.9600 - 1.9000 1.00 2148 141 0.2067 0.2607 REMARK 3 12 1.9000 - 1.8400 1.00 2137 140 0.2181 0.2233 REMARK 3 13 1.8400 - 1.7900 1.00 2146 141 0.2167 0.2523 REMARK 3 14 1.7900 - 1.7500 0.98 2102 138 0.2392 0.2777 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.75 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 : 0.010 1855 REMARK 3 ANGLE : 1.047 2520 REMARK 3 CHIRALITY : 0.068 285 REMARK 3 PLANARITY : 0.008 341 REMARK 3 DIHEDRAL : 12.320 702 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 7SE7 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_1000258887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-18 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 : MX1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32353 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 47.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 58.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 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 32.83250 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 32.83250 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 34.63800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.46200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.63800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.46200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.83250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.63800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.46200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.83250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.63800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.46200 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 ARG A 100 REMARK 465 GLY A 101 REMARK 465 LYS A 102 REMARK 465 GLU A 103 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: 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 H GLY A 128 O HOH A 505 1.60 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 HIS A 156 -30.10 72.88 REMARK 500 ALA A 169 -134.85 55.20 REMARK 500 ASP A 236 56.48 -151.63 REMARK 500 ASP A 270 101.36 -160.05 REMARK 500 REMARK 500 REMARK: NULL DBREF 7SE7 A 83 321 UNP P22087 FBRL_HUMAN 83 321 SEQADV 7SE7 SER A 80 UNP P22087 EXPRESSION TAG SEQADV 7SE7 ASN A 81 UNP P22087 EXPRESSION TAG SEQADV 7SE7 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 SAM A 401 49 HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 HOH *189(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 GLU A 289 1 16 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 LEU A 106 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 VAL A 213 SHEET 3 AA2 7 LYS A 162 LEU A 166 1 N VAL A 163 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 TYR A 313 N GLY A 257 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 4.12 CRYST1 69.276 138.924 65.665 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 0.014435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015229 0.00000