HEADER TRANSFERASE 09-SEP-22 8GU3 TITLE CRYSTAL STRUCTURE OF CAENORHABDITIS ELEGANS METT-10 METHYLTRANSFERASE TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: U6 SMALL NUCLEAR RNA (ADENINE-(43)-N(6))-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N6-ADENOSINE-METHYLTRANSFERASE METT-10; COMPND 5 EC: 2.1.1.346; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: METT-10; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SAM HOMEOSTASIS, U6 SNRNA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.JU,K.TOMITA REVDAT 4 29-NOV-23 8GU3 1 REMARK REVDAT 3 29-MAR-23 8GU3 1 JRNL REVDAT 2 01-MAR-23 8GU3 1 JRNL REVDAT 1 01-FEB-23 8GU3 0 JRNL AUTH J.JU,T.AOYAMA,Y.YASHIRO,S.YAMASHITA,H.KUROYANAGI,K.TOMITA JRNL TITL STRUCTURE OF THE CAENORHABDITIS ELEGANS M6A JRNL TITL 2 METHYLTRANSFERASE METT10 THAT REGULATES SAM HOMEOSTASIS. JRNL REF NUCLEIC ACIDS RES. V. 51 2434 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36794723 JRNL DOI 10.1093/NAR/GKAD081 REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6085 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 305 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 47.1200 - 3.7900 1.00 2949 156 0.2332 0.2856 REMARK 3 2 3.7900 - 3.0100 1.00 2831 149 0.2688 0.3405 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 103.7 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -23.7015 -0.4210 -9.7799 REMARK 3 T TENSOR REMARK 3 T11: 0.5512 T22: 0.6411 REMARK 3 T33: 0.7041 T12: 0.1720 REMARK 3 T13: 0.1763 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 2.3797 L22: 8.7535 REMARK 3 L33: 5.3709 L12: -1.4799 REMARK 3 L13: 1.9121 L23: -4.9607 REMARK 3 S TENSOR REMARK 3 S11: -0.3086 S12: -0.5257 S13: 0.0505 REMARK 3 S21: 0.8014 S22: 0.8218 S23: 0.1623 REMARK 3 S31: -1.1309 S32: -0.6587 S33: -0.3372 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 8GU3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031492. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6086 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.010 REMARK 200 RESOLUTION RANGE LOW (A) : 47.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.54 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 12.38 REMARK 200 R MERGE FOR SHELL (I) : 1.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.590 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: 6B91 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, TRIS-HCL PH8.5, PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING 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 21.60500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.11500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.04000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.11500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.60500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.04000 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 ASN A 4 REMARK 465 ASN A 5 REMARK 465 PHE A 188 REMARK 465 GLU A 189 REMARK 465 LYS A 190 REMARK 465 GLY A 191 REMARK 465 ASN A 192 REMARK 465 GLY A 193 REMARK 465 ASP A 194 REMARK 465 ASP A 195 REMARK 465 LYS A 196 REMARK 465 PHE A 197 REMARK 465 CYS A 198 REMARK 465 GLU A 199 REMARK 465 ASP A 200 REMARK 465 ILE A 201 REMARK 465 SER A 202 REMARK 465 SER A 203 REMARK 465 SER A 204 REMARK 465 THR A 205 REMARK 465 GLU A 206 REMARK 465 THR A 207 REMARK 465 TYR A 208 REMARK 465 SER A 209 REMARK 465 ASN A 210 REMARK 465 ARG A 211 REMARK 465 VAL A 212 REMARK 465 ALA A 213 REMARK 465 SER A 214 REMARK 465 GLU A 215 REMARK 465 PHE A 216 REMARK 465 ARG A 217 REMARK 465 THR A 218 REMARK 465 ALA A 219 REMARK 465 PRO A 220 REMARK 465 HIS A 221 REMARK 465 SER A 222 REMARK 465 ALA A 223 REMARK 465 THR A 224 REMARK 465 PHE A 225 REMARK 465 ALA A 226 REMARK 465 SER A 227 REMARK 465 SER A 228 REMARK 465 ALA A 229 REMARK 465 GLU A 230 REMARK 465 LEU A 231 REMARK 465 PHE A 232 REMARK 465 VAL A 233 REMARK 465 ASP A 234 REMARK 465 GLY A 235 REMARK 465 THR A 310 REMARK 465 THR A 311 REMARK 465 ILE A 312 REMARK 465 ASP A 313 REMARK 465 ARG A 314 REMARK 465 LEU A 315 REMARK 465 GLU A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 HIS A 321 REMARK 465 HIS A 322 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 38 0.97 -69.63 REMARK 500 GLN A 291 -8.45 74.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GU3 A 1 314 UNP Q09357 MET16_CAEEL 1 314 SEQADV 8GU3 LEU A 315 UNP Q09357 EXPRESSION TAG SEQADV 8GU3 GLU A 316 UNP Q09357 EXPRESSION TAG SEQADV 8GU3 HIS A 317 UNP Q09357 EXPRESSION TAG SEQADV 8GU3 HIS A 318 UNP Q09357 EXPRESSION TAG SEQADV 8GU3 HIS A 319 UNP Q09357 EXPRESSION TAG SEQADV 8GU3 HIS A 320 UNP Q09357 EXPRESSION TAG SEQADV 8GU3 HIS A 321 UNP Q09357 EXPRESSION TAG SEQADV 8GU3 HIS A 322 UNP Q09357 EXPRESSION TAG SEQRES 1 A 322 MET SER GLN ASN ASN GLU MET HIS PRO ARG ASN PRO TYR SEQRES 2 A 322 ARG ASN LYS PRO PRO ASP PHE LYS ALA LEU ALA VAL GLU SEQRES 3 A 322 TYR PRO GLU PHE ARG LYS PHE CYS GLN TYR VAL SER ASN SEQRES 4 A 322 GLY LYS VAL THR PHE ASP PHE LYS LYS ASP ALA ALA VAL SEQRES 5 A 322 ARG CYS LEU THR GLN THR LEU LEU LYS LYS ASP PHE ASN SEQRES 6 A 322 LEU ASP VAL GLU ILE PRO PRO GLY HIS LEU VAL PRO ARG SEQRES 7 A 322 VAL PRO GLN LYS LEU ASN TYR CYS LEU LEU ILE ASP ASP SEQRES 8 A 322 LEU LEU LYS ALA ASN LYS LEU THR LYS ASN VAL ILE GLY SEQRES 9 A 322 ILE ASP ILE GLY THR GLY THR SER CYS ILE HIS ALA LEU SEQRES 10 A 322 ILE GLY ALA ARG GLN PHE ASN TRP LYS PHE ILE ALA THR SEQRES 11 A 322 ASP GLY ASP GLU LYS SER VAL ARG VAL ALA HIS GLU ASN SEQRES 12 A 322 VAL ALA LYS ASN GLY LEU SER SER SER ILE CYS VAL VAL SEQRES 13 A 322 HIS VAL ASN PRO ASP VAL LYS THR VAL LEU MET ASP VAL SEQRES 14 A 322 VAL ASN THR ILE PRO ASP THR ASP TYR ALA PHE CYS MET SEQRES 15 A 322 CYS ASN PRO PRO PHE PHE GLU LYS GLY ASN GLY ASP ASP SEQRES 16 A 322 LYS PHE CYS GLU ASP ILE SER SER SER THR GLU THR TYR SEQRES 17 A 322 SER ASN ARG VAL ALA SER GLU PHE ARG THR ALA PRO HIS SEQRES 18 A 322 SER ALA THR PHE ALA SER SER ALA GLU LEU PHE VAL ASP SEQRES 19 A 322 GLY GLY GLU VAL ALA PHE VAL ASN ARG ILE ILE ASP ASP SEQRES 20 A 322 SER VAL LEU LEU ARG ASP ARG ILE LYS ILE TYR THR THR SEQRES 21 A 322 MET ILE GLY ARG LYS SER SER LEU LYS PRO LEU GLN ASN SEQRES 22 A 322 ARG LEU GLN ARG PHE GLY ASP ASP VAL LYS ILE MET ILE SEQRES 23 A 322 SER VAL LEU ASN GLN GLY LYS THR LYS ARG TRP MET LEU SEQRES 24 A 322 ALA TRP THR PHE SER LYS SER VAL SER LEU THR THR ILE SEQRES 25 A 322 ASP ARG LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASP A 19 TYR A 27 1 9 HELIX 2 AA2 TYR A 27 LYS A 32 1 6 HELIX 3 AA3 LYS A 48 ASN A 65 1 18 HELIX 4 AA4 ARG A 78 ASN A 96 1 19 HELIX 5 AA5 CYS A 113 PHE A 123 1 11 HELIX 6 AA6 ASP A 133 GLY A 148 1 16 HELIX 7 AA7 LEU A 166 ASN A 171 1 6 HELIX 8 AA8 GLU A 237 LEU A 250 1 14 HELIX 9 AA9 ARG A 264 SER A 266 5 3 HELIX 10 AB1 SER A 267 ARG A 277 1 11 HELIX 11 AB2 PHE A 278 VAL A 282 5 5 SHEET 1 AA1 7 ILE A 153 HIS A 157 0 SHEET 2 AA1 7 LYS A 126 ASP A 131 1 N ALA A 129 O VAL A 156 SHEET 3 AA1 7 ILE A 103 ILE A 107 1 N GLY A 104 O LYS A 126 SHEET 4 AA1 7 PHE A 180 CYS A 183 1 O MET A 182 N ILE A 105 SHEET 5 AA1 7 ILE A 257 ILE A 262 1 O MET A 261 N CYS A 183 SHEET 6 AA1 7 TRP A 297 THR A 302 -1 O LEU A 299 N THR A 260 SHEET 7 AA1 7 LYS A 283 VAL A 288 -1 N MET A 285 O ALA A 300 CRYST1 43.210 70.080 94.230 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 0.023143 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014269 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010612 0.00000