HEADER TRANSFERASE 08-OCT-20 7D8F TITLE THE CRYSTAL STRUCTURE OF SCNTM1 IN COMPLEX WITH SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA N-TERMINAL PROTEIN METHYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSLATION ASSOCIATED ELEMENT 1,X-PRO-LYS N-TERMINAL COMPND 5 PROTEIN METHYLTRANSFERASE 1,NTM1; COMPND 6 EC: 2.1.1.244; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_TAXID: 4932; SOURCE 4 GENE: TAE1, NTM1, YBR261C, YBR1729; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SCNTM1, N-TERMINAL METHYLATION, METHYLTRANSFERASE, SACCHAROMYCES KEYWDS 2 CEREVISIAE, SUBSTRATE BINDING POCKET, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.Y.ZHANG,J.YUE,Z.L.ZHU REVDAT 3 29-NOV-23 7D8F 1 REMARK REVDAT 2 29-DEC-21 7D8F 1 JRNL REVDAT 1 26-MAY-21 7D8F 0 JRNL AUTH H.Y.ZHANG,Z.KUANG,L.XUE,J.YUE,M.H.KHAN,Z.ZHU,L.NIU JRNL TITL STRUCTURAL BASIS FOR PEPTIDE BINDING OF ALPHA-N TERMINAL JRNL TITL 2 METHYLTRANSFERASE FROM SACCHAROMYCES CEREVISIAE JRNL REF CRYSTALLOGRAPHY REPORTS V. 66 1316 2021 JRNL REFN ISSN 1063-7745 JRNL DOI 10.1134/S1063774521070257 REMARK 2 REMARK 2 RESOLUTION. 1.15 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 82645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.140 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 4155 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 23.9100 - 3.1200 1.00 4390 245 0.1467 0.1575 REMARK 3 2 3.1200 - 2.4800 1.00 4220 211 0.1304 0.1451 REMARK 3 3 2.4800 - 2.1600 1.00 4161 219 0.1179 0.1355 REMARK 3 4 2.1600 - 1.9700 1.00 4152 222 0.1108 0.1218 REMARK 3 5 1.9700 - 1.8300 1.00 4093 248 0.1145 0.1436 REMARK 3 6 1.8300 - 1.7200 1.00 4125 212 0.1124 0.1155 REMARK 3 7 1.7200 - 1.6300 1.00 4063 248 0.1043 0.1302 REMARK 3 8 1.6300 - 1.5600 1.00 4127 202 0.1006 0.1269 REMARK 3 9 1.5600 - 1.5000 1.00 4084 187 0.0989 0.1151 REMARK 3 10 1.5000 - 1.4500 1.00 4067 243 0.1035 0.1334 REMARK 3 11 1.4500 - 1.4000 1.00 4074 223 0.1098 0.1357 REMARK 3 12 1.4000 - 1.3600 1.00 4089 205 0.1084 0.1340 REMARK 3 13 1.3600 - 1.3300 1.00 4053 218 0.1028 0.1371 REMARK 3 14 1.3300 - 1.3000 1.00 4104 205 0.1019 0.1386 REMARK 3 15 1.3000 - 1.2700 1.00 4065 211 0.1078 0.1299 REMARK 3 16 1.2700 - 1.2400 1.00 3993 216 0.1127 0.1265 REMARK 3 17 1.2400 - 1.2100 0.90 3677 194 0.1243 0.1562 REMARK 3 18 1.2100 - 1.1900 0.81 3273 188 0.1425 0.1618 REMARK 3 19 1.1900 - 1.1700 0.73 2953 132 0.1705 0.1908 REMARK 3 20 1.1700 - 1.1500 0.64 2618 126 0.1976 0.2232 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) : 0.077 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.321 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.96 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 : 0.007 1981 REMARK 3 ANGLE : 1.058 2703 REMARK 3 CHIRALITY : 0.081 296 REMARK 3 PLANARITY : 0.007 351 REMARK 3 DIHEDRAL : 19.873 762 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 7D8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1300015418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 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 : HKL-2000 1.10.1_2155 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88586 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 42.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 2EX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M SODIUM ACETATE TRIHYDRATE PH 7.0, REMARK 280 3.5M SODIUM FORMATE PH 7.0, 20% PEG3350,0.2M MAGNESIUM NITRATE REMARK 280 HEXAHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 19.20100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.00850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.07400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.00850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.20100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.07400 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 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 TYR A 32 61.25 -103.08 REMARK 500 MET A 81 -62.78 -145.75 REMARK 500 CYS A 141 -22.59 -144.58 REMARK 500 ASP A 177 39.86 -81.99 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 667 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 668 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A 669 DISTANCE = 6.72 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 301 DBREF 7D8F A 1 232 UNP P38340 NTM1_YEAST 1 232 SEQADV 7D8F HIS A -1 UNP P38340 EXPRESSION TAG SEQADV 7D8F HIS A 0 UNP P38340 EXPRESSION TAG SEQRES 1 A 234 HIS HIS MET ASP VAL PRO ALA ASP SER HIS ILE LYS TYR SEQRES 2 A 234 GLU ASP ALA ILE ASP TYR TRP THR ASP VAL ASP ALA THR SEQRES 3 A 234 VAL ASP GLY VAL LEU GLY GLY TYR GLY GLU GLY THR VAL SEQRES 4 A 234 VAL PRO THR MET ASP VAL LEU GLY SER ASN ASN PHE LEU SEQRES 5 A 234 ARG LYS LEU LYS SER ARG MET LEU PRO GLN GLU ASN ASN SEQRES 6 A 234 VAL LYS TYR ALA VAL ASP ILE GLY ALA GLY ILE GLY ARG SEQRES 7 A 234 VAL SER LYS THR MET LEU HIS LYS HIS ALA ALA LYS ILE SEQRES 8 A 234 ASP LEU VAL GLU PRO VAL LYS PRO PHE ILE GLU GLN MET SEQRES 9 A 234 HIS VAL GLU LEU ALA GLU LEU LYS ASP LYS GLY GLN ILE SEQRES 10 A 234 GLY GLN ILE TYR GLU VAL GLY MET GLN ASP TRP THR PRO SEQRES 11 A 234 ASP ALA GLY LYS TYR TRP LEU ILE TRP CYS GLN TRP CYS SEQRES 12 A 234 VAL GLY HIS LEU PRO ASP ALA GLU LEU VAL ALA PHE LEU SEQRES 13 A 234 LYS ARG CYS ILE VAL GLY LEU GLN PRO ASN GLY THR ILE SEQRES 14 A 234 VAL VAL LYS GLU ASN ASN THR PRO THR ASP THR ASP ASP SEQRES 15 A 234 PHE ASP GLU THR ASP SER SER VAL THR ARG SER ASP ALA SEQRES 16 A 234 LYS PHE ARG GLN ILE PHE GLU GLU ALA GLY LEU LYS LEU SEQRES 17 A 234 ILE ALA SER GLU ARG GLN ARG GLY LEU PRO ARG GLU LEU SEQRES 18 A 234 TYR PRO VAL ARG MET TYR ALA LEU LYS PRO MET PRO ASN HET SAH A 301 45 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *269(H2 O) HELIX 1 AA1 PRO A 4 ILE A 9 5 6 HELIX 2 AA2 LYS A 10 ASP A 20 1 11 HELIX 3 AA3 THR A 24 LEU A 29 1 6 HELIX 4 AA4 VAL A 37 LEU A 53 1 17 HELIX 5 AA5 LYS A 54 MET A 57 5 4 HELIX 6 AA6 GLY A 75 MET A 81 1 7 HELIX 7 AA7 MET A 81 ALA A 86 1 6 HELIX 8 AA8 VAL A 95 LEU A 106 1 12 HELIX 9 AA9 LEU A 106 LYS A 112 1 7 HELIX 10 AB1 GLY A 122 TRP A 126 5 5 HELIX 11 AB2 CYS A 141 LEU A 145 5 5 HELIX 12 AB3 PRO A 146 GLY A 160 1 15 HELIX 13 AB4 SER A 191 ALA A 202 1 12 SHEET 1 AA1 7 ILE A 115 TYR A 119 0 SHEET 2 AA1 7 LYS A 88 VAL A 92 1 N LEU A 91 O TYR A 119 SHEET 3 AA1 7 TYR A 66 ILE A 70 1 N ALA A 67 O LYS A 88 SHEET 4 AA1 7 TYR A 133 GLN A 139 1 O TRP A 137 N ILE A 70 SHEET 5 AA1 7 LEU A 161 ASN A 172 1 O VAL A 168 N CYS A 138 SHEET 6 AA1 7 VAL A 222 PRO A 229 -1 O LEU A 227 N ILE A 167 SHEET 7 AA1 7 LEU A 204 ARG A 211 -1 N LYS A 205 O LYS A 228 SHEET 1 AA2 2 ASP A 180 ASP A 182 0 SHEET 2 AA2 2 SER A 187 THR A 189 -1 O SER A 187 N ASP A 182 SITE 1 AC1 20 TRP A 18 GLY A 71 ALA A 72 GLY A 73 SITE 2 AC1 20 ARG A 76 VAL A 77 GLU A 93 PRO A 94 SITE 3 AC1 20 VAL A 95 PHE A 98 GLY A 122 MET A 123 SITE 4 AC1 20 GLN A 124 GLN A 139 TRP A 140 CYS A 141 SITE 5 AC1 20 HIS A 144 HOH A 421 HOH A 476 HOH A 524 CRYST1 38.402 52.148 120.017 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 0.026040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019176 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008332 0.00000