HEADER TRANSFERASE 07-JUL-22 7YF4 TITLE CRYSTAL STRUCTURE OF METTL9 IN COMPLEX WITH SLC39A5 MUTANT PEPTIDE AND TITLE 2 SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-L-HISTIDINE N-PROS-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DORA REVERSE STRAND PROTEIN,DREV,DREV1,METHYLTRANSFERASE- COMPND 5 LIKE PROTEIN 9,HMETTL9, METTL9; COMPND 6 EC: 2.1.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SLC39A5 MUTANT PEPTIDE; COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: METTL9, DREV, CGI-81; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: METTL9, DREV, CGI-81; SOURCE 13 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS METTL9, SLC39A5, HISTIDINE METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.XIE,X.WANG,C.XU REVDAT 3 08-MAY-24 7YF4 1 JRNL REVDAT 2 29-NOV-23 7YF4 1 REMARK REVDAT 1 12-APR-23 7YF4 0 JRNL AUTH X.WANG,H.XIE,Q.GUO,D.CAO,W.RU,S.ZHAO,Z.ZHU,J.ZHANG,W.PAN, JRNL AUTH 2 X.YAO,C.XU JRNL TITL MOLECULAR BASIS FOR METTL9-MEDIATED N1-HISTIDINE JRNL TITL 2 METHYLATION. JRNL REF CELL DISCOV V. 9 38 2023 JRNL REFN ESSN 2056-5968 JRNL PMID 37015930 JRNL DOI 10.1038/S41421-023-00548-W REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487) 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 14118 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1412 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 59.8600 - 5.9200 0.99 1360 151 0.1823 0.2207 REMARK 3 2 5.9200 - 4.7000 1.00 1327 148 0.2085 0.2313 REMARK 3 3 4.7000 - 4.1000 1.00 1307 145 0.1813 0.2491 REMARK 3 4 4.1000 - 3.7300 0.93 1205 134 0.2234 0.2902 REMARK 3 5 3.7300 - 3.4600 0.89 1169 130 0.2389 0.3456 REMARK 3 6 3.4600 - 3.2600 0.92 1180 132 0.2379 0.3175 REMARK 3 7 3.2600 - 3.0900 1.00 1262 140 0.2571 0.3613 REMARK 3 8 3.0900 - 2.9600 1.00 1332 147 0.2813 0.4028 REMARK 3 9 2.9600 - 2.8500 1.00 1285 143 0.3185 0.3893 REMARK 3 10 2.8500 - 2.7500 1.00 1279 142 0.3242 0.4177 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.22 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 : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 54:318 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.346 -6.348 15.131 REMARK 3 T TENSOR REMARK 3 T11: 0.3780 T22: 0.4709 REMARK 3 T33: 0.3739 T12: 0.0044 REMARK 3 T13: -0.0004 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 1.1512 L22: 1.2281 REMARK 3 L33: 1.3083 L12: 0.5005 REMARK 3 L13: 0.4986 L23: 0.2584 REMARK 3 S TENSOR REMARK 3 S11: 0.0195 S12: -0.1337 S13: 0.0407 REMARK 3 S21: -0.1826 S22: 0.0367 S23: 0.0238 REMARK 3 S31: -0.1276 S32: 0.0051 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND RESID 55:318 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.779 -24.549 29.405 REMARK 3 T TENSOR REMARK 3 T11: 0.3866 T22: 0.7033 REMARK 3 T33: 0.4327 T12: -0.0647 REMARK 3 T13: -0.0176 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 1.6563 L22: 1.0118 REMARK 3 L33: 1.3099 L12: 0.5691 REMARK 3 L13: -0.0172 L23: -0.2783 REMARK 3 S TENSOR REMARK 3 S11: 0.1301 S12: -0.3331 S13: -0.1049 REMARK 3 S21: 0.1084 S22: -0.1578 S23: -0.0381 REMARK 3 S31: 0.0524 S32: 0.0550 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN C AND RESID -3:3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.008 -3.860 5.774 REMARK 3 T TENSOR REMARK 3 T11: 0.5324 T22: 0.8113 REMARK 3 T33: 0.4180 T12: -0.0272 REMARK 3 T13: 0.0212 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.0039 L22: 0.0133 REMARK 3 L33: 0.0008 L12: 0.0019 REMARK 3 L13: -0.0048 L23: -0.0054 REMARK 3 S TENSOR REMARK 3 S11: 0.0481 S12: 0.0689 S13: 0.1899 REMARK 3 S21: -0.3314 S22: 0.3366 S23: 0.2945 REMARK 3 S31: -0.2004 S32: -0.0705 S33: 0.0025 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN D AND RESID -3:2 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.927 -31.318 19.436 REMARK 3 T TENSOR REMARK 3 T11: 0.6871 T22: 0.6762 REMARK 3 T33: 0.7543 T12: 0.0420 REMARK 3 T13: -0.0421 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 0.0120 L22: 0.0154 REMARK 3 L33: 0.0590 L12: 0.0055 REMARK 3 L13: -0.0070 L23: -0.0195 REMARK 3 S TENSOR REMARK 3 S11: -0.1177 S12: -0.0457 S13: -0.0237 REMARK 3 S21: 0.0013 S22: -0.2393 S23: -0.2283 REMARK 3 S31: -0.1294 S32: -0.0678 S33: -0.0008 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 401:401 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.613 -7.722 17.137 REMARK 3 T TENSOR REMARK 3 T11: 0.7187 T22: 0.7136 REMARK 3 T33: 0.5293 T12: 0.0826 REMARK 3 T13: 0.0342 T23: 0.1439 REMARK 3 L TENSOR REMARK 3 L11: 0.1011 L22: 0.0262 REMARK 3 L33: 0.1455 L12: 0.0184 REMARK 3 L13: -0.1143 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.1620 S12: -0.0722 S13: -0.0005 REMARK 3 S21: 0.0002 S22: -0.1405 S23: 0.3161 REMARK 3 S31: 0.1597 S32: -0.0488 S33: -0.0015 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN B AND RESID 401:401 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.544 -21.912 26.649 REMARK 3 T TENSOR REMARK 3 T11: 0.6424 T22: 0.9174 REMARK 3 T33: 0.5484 T12: 0.0265 REMARK 3 T13: -0.1595 T23: 0.1118 REMARK 3 L TENSOR REMARK 3 L11: 0.2989 L22: 0.0816 REMARK 3 L33: 0.0189 L12: 0.1332 REMARK 3 L13: 0.0720 L23: 0.0370 REMARK 3 S TENSOR REMARK 3 S11: -0.0978 S12: 0.0027 S13: -0.0252 REMARK 3 S21: -0.1165 S22: -0.2260 S23: 0.1193 REMARK 3 S31: 0.0369 S32: 0.0503 S33: 0.0003 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 7YF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-22 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14118 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 59.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: PHASER REMARK 200 STARTING MODEL: 7YF2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE PH6.5, 12% W/V REMARK 280 PEG 20000, 0.2 M SODIUM THIOCYANATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 71.19350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.60650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.19350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.60650 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 HIS A 44 REMARK 465 MET A 45 REMARK 465 ALA A 46 REMARK 465 ALA A 47 REMARK 465 GLY A 48 REMARK 465 GLY A 49 REMARK 465 ARG A 50 REMARK 465 LYS A 51 REMARK 465 GLU A 52 REMARK 465 ASN A 53 REMARK 465 HIS B 44 REMARK 465 MET B 45 REMARK 465 ALA B 46 REMARK 465 ALA B 47 REMARK 465 GLY B 48 REMARK 465 GLY B 49 REMARK 465 ARG B 50 REMARK 465 LYS B 51 REMARK 465 GLU B 52 REMARK 465 ASN B 53 REMARK 465 HIS B 54 REMARK 465 THR B 199 REMARK 465 GLY B 200 REMARK 465 PHE B 201 REMARK 465 GLY C -5 REMARK 465 HIS C -4 REMARK 465 GLN C 4 REMARK 465 GLY C 5 REMARK 465 GLY C 6 REMARK 465 GLY D -5 REMARK 465 HIS D -4 REMARK 465 HIS D 3 REMARK 465 GLN D 4 REMARK 465 GLY D 5 REMARK 465 GLY D 6 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 GLN A 55 CG CD OE1 NE2 REMARK 470 GLU A 62 CG CD OE1 OE2 REMARK 470 GLU A 66 CG CD OE1 OE2 REMARK 470 LYS A 91 CG CD CE NZ REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 LYS A 223 CG CD CE NZ REMARK 470 HIS A 245 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 GLU A 256 CG CD OE1 OE2 REMARK 470 LYS A 257 CG CD CE NZ REMARK 470 GLU A 278 CG CD OE1 OE2 REMARK 470 LYS A 316 CG CD CE NZ REMARK 470 GLN B 55 CG CD OE1 NE2 REMARK 470 ARG B 136 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 147 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 161 CG CD CE NZ REMARK 470 GLU B 168 CG CD OE1 OE2 REMARK 470 ARG B 189 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 202 CG CD OE1 NE2 REMARK 470 LYS B 223 CG CD CE NZ REMARK 470 LYS B 254 CG CD CE NZ REMARK 470 GLU B 256 CG CD OE1 OE2 REMARK 470 LYS B 257 CG CD CE NZ REMARK 470 LYS B 316 CG CD CE NZ 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 LYS A 139 75.02 54.42 REMARK 500 CYS A 208 65.74 -150.26 REMARK 500 ASN A 250 -164.25 -113.65 REMARK 500 GLU A 263 71.22 -103.34 REMARK 500 ASP A 300 -150.21 -124.19 REMARK 500 ASN B 60 95.17 -68.25 REMARK 500 SER B 92 21.51 -76.38 REMARK 500 GLU B 174 149.21 -171.95 REMARK 500 ASP B 300 -115.04 -125.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YF4 A 46 318 UNP Q9H1A3 METL9_HUMAN 46 318 DBREF 7YF4 B 46 318 UNP Q9H1A3 METL9_HUMAN 46 318 DBREF 7YF4 C -5 6 PDB 7YF4 7YF4 -5 6 DBREF 7YF4 D -5 6 PDB 7YF4 7YF4 -5 6 SEQADV 7YF4 HIS A 44 UNP Q9H1A3 EXPRESSION TAG SEQADV 7YF4 MET A 45 UNP Q9H1A3 EXPRESSION TAG SEQADV 7YF4 ALA A 95 UNP Q9H1A3 LEU 95 ENGINEERED MUTATION SEQADV 7YF4 ALA A 96 UNP Q9H1A3 PHE 96 ENGINEERED MUTATION SEQADV 7YF4 ALA A 99 UNP Q9H1A3 LEU 99 ENGINEERED MUTATION SEQADV 7YF4 ALA A 103 UNP Q9H1A3 PHE 103 ENGINEERED MUTATION SEQADV 7YF4 ALA A 107 UNP Q9H1A3 VAL 107 ENGINEERED MUTATION SEQADV 7YF4 ALA A 111 UNP Q9H1A3 PHE 111 ENGINEERED MUTATION SEQADV 7YF4 HIS B 44 UNP Q9H1A3 EXPRESSION TAG SEQADV 7YF4 MET B 45 UNP Q9H1A3 EXPRESSION TAG SEQADV 7YF4 ALA B 95 UNP Q9H1A3 LEU 95 ENGINEERED MUTATION SEQADV 7YF4 ALA B 96 UNP Q9H1A3 PHE 96 ENGINEERED MUTATION SEQADV 7YF4 ALA B 99 UNP Q9H1A3 LEU 99 ENGINEERED MUTATION SEQADV 7YF4 ALA B 103 UNP Q9H1A3 PHE 103 ENGINEERED MUTATION SEQADV 7YF4 ALA B 107 UNP Q9H1A3 VAL 107 ENGINEERED MUTATION SEQADV 7YF4 ALA B 111 UNP Q9H1A3 PHE 111 ENGINEERED MUTATION SEQRES 1 A 275 HIS MET ALA ALA GLY GLY ARG LYS GLU ASN HIS GLN TRP SEQRES 2 A 275 TYR VAL CYS ASN ARG GLU LYS LEU CYS GLU SER LEU GLN SEQRES 3 A 275 ALA VAL PHE VAL GLN SER TYR LEU ASP GLN GLY THR GLN SEQRES 4 A 275 ILE PHE LEU ASN ASN SER ILE GLU LYS SER GLY TRP ALA SEQRES 5 A 275 ALA ILE GLN ALA TYR HIS SER ALA VAL SER SER ALA PHE SEQRES 6 A 275 SER LEU ALA MET SER ARG THR SER ILE ASN GLY LEU LEU SEQRES 7 A 275 GLY ARG GLY SER MET PHE VAL PHE SER PRO ASP GLN PHE SEQRES 8 A 275 GLN ARG LEU LEU LYS ILE ASN PRO ASP TRP LYS THR HIS SEQRES 9 A 275 ARG LEU LEU ASP LEU GLY ALA GLY ASP GLY GLU VAL THR SEQRES 10 A 275 LYS ILE MET SER PRO HIS PHE GLU GLU ILE TYR ALA THR SEQRES 11 A 275 GLU LEU SER GLU THR MET ILE TRP GLN LEU GLN LYS LYS SEQRES 12 A 275 LYS TYR ARG VAL LEU GLY ILE ASN GLU TRP GLN ASN THR SEQRES 13 A 275 GLY PHE GLN TYR ASP VAL ILE SER CYS LEU ASN LEU LEU SEQRES 14 A 275 ASP ARG CYS ASP GLN PRO LEU THR LEU LEU LYS ASP ILE SEQRES 15 A 275 ARG SER VAL LEU GLU PRO THR ARG GLY ARG VAL ILE LEU SEQRES 16 A 275 ALA LEU VAL LEU PRO PHE HIS PRO TYR VAL GLU ASN VAL SEQRES 17 A 275 GLY GLY LYS TRP GLU LYS PRO SER GLU ILE LEU GLU ILE SEQRES 18 A 275 LYS GLY GLN ASN TRP GLU GLU GLN VAL ASN SER LEU PRO SEQRES 19 A 275 GLU VAL PHE ARG LYS ALA GLY PHE VAL ILE GLU ALA PHE SEQRES 20 A 275 THR ARG LEU PRO TYR LEU CYS GLU GLY ASP MET TYR ASN SEQRES 21 A 275 ASP TYR TYR VAL LEU ASP ASP ALA VAL PHE VAL LEU LYS SEQRES 22 A 275 PRO VAL SEQRES 1 B 275 HIS MET ALA ALA GLY GLY ARG LYS GLU ASN HIS GLN TRP SEQRES 2 B 275 TYR VAL CYS ASN ARG GLU LYS LEU CYS GLU SER LEU GLN SEQRES 3 B 275 ALA VAL PHE VAL GLN SER TYR LEU ASP GLN GLY THR GLN SEQRES 4 B 275 ILE PHE LEU ASN ASN SER ILE GLU LYS SER GLY TRP ALA SEQRES 5 B 275 ALA ILE GLN ALA TYR HIS SER ALA VAL SER SER ALA PHE SEQRES 6 B 275 SER LEU ALA MET SER ARG THR SER ILE ASN GLY LEU LEU SEQRES 7 B 275 GLY ARG GLY SER MET PHE VAL PHE SER PRO ASP GLN PHE SEQRES 8 B 275 GLN ARG LEU LEU LYS ILE ASN PRO ASP TRP LYS THR HIS SEQRES 9 B 275 ARG LEU LEU ASP LEU GLY ALA GLY ASP GLY GLU VAL THR SEQRES 10 B 275 LYS ILE MET SER PRO HIS PHE GLU GLU ILE TYR ALA THR SEQRES 11 B 275 GLU LEU SER GLU THR MET ILE TRP GLN LEU GLN LYS LYS SEQRES 12 B 275 LYS TYR ARG VAL LEU GLY ILE ASN GLU TRP GLN ASN THR SEQRES 13 B 275 GLY PHE GLN TYR ASP VAL ILE SER CYS LEU ASN LEU LEU SEQRES 14 B 275 ASP ARG CYS ASP GLN PRO LEU THR LEU LEU LYS ASP ILE SEQRES 15 B 275 ARG SER VAL LEU GLU PRO THR ARG GLY ARG VAL ILE LEU SEQRES 16 B 275 ALA LEU VAL LEU PRO PHE HIS PRO TYR VAL GLU ASN VAL SEQRES 17 B 275 GLY GLY LYS TRP GLU LYS PRO SER GLU ILE LEU GLU ILE SEQRES 18 B 275 LYS GLY GLN ASN TRP GLU GLU GLN VAL ASN SER LEU PRO SEQRES 19 B 275 GLU VAL PHE ARG LYS ALA GLY PHE VAL ILE GLU ALA PHE SEQRES 20 B 275 THR ARG LEU PRO TYR LEU CYS GLU GLY ASP MET TYR ASN SEQRES 21 B 275 ASP TYR TYR VAL LEU ASP ASP ALA VAL PHE VAL LEU LYS SEQRES 22 B 275 PRO VAL SEQRES 1 C 12 GLY HIS GLN GLY HIS ALA HIS GLY HIS GLN GLY GLY SEQRES 1 D 12 GLY HIS GLN GLY HIS ALA HIS GLY HIS GLN GLY GLY HET SAH A 401 26 HET SAH B 401 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 5 SAH 2(C14 H20 N6 O5 S) FORMUL 7 HOH *7(H2 O) HELIX 1 AA1 ASN A 60 LEU A 64 5 5 HELIX 2 AA2 CYS A 65 ALA A 70 1 6 HELIX 3 AA3 ASP A 78 GLY A 93 1 16 HELIX 4 AA4 TRP A 94 PHE A 108 1 15 HELIX 5 AA5 SER A 113 GLY A 122 1 10 HELIX 6 AA6 SER A 130 LYS A 139 1 10 HELIX 7 AA7 VAL A 159 SER A 164 1 6 HELIX 8 AA8 SER A 176 LYS A 186 1 11 HELIX 9 AA9 GLU A 195 THR A 199 5 5 HELIX 10 AB1 GLN A 217 LEU A 229 1 13 HELIX 11 AB2 ASN A 268 SER A 275 1 8 HELIX 12 AB3 SER A 275 ALA A 283 1 9 HELIX 13 AB4 ASN B 60 LEU B 64 5 5 HELIX 14 AB5 CYS B 65 ALA B 70 1 6 HELIX 15 AB6 ASP B 78 SER B 92 1 15 HELIX 16 AB7 TRP B 94 SER B 109 1 16 HELIX 17 AB8 SER B 113 GLY B 122 1 10 HELIX 18 AB9 SER B 130 LYS B 139 1 10 HELIX 19 AC1 GLY B 157 ILE B 162 1 6 HELIX 20 AC2 MET B 163 PRO B 165 5 3 HELIX 21 AC3 SER B 176 LYS B 186 1 11 HELIX 22 AC4 GLN B 217 VAL B 228 1 12 HELIX 23 AC5 VAL B 251 GLY B 253 5 3 HELIX 24 AC6 ASN B 268 SER B 275 1 8 HELIX 25 AC7 LEU B 276 GLY B 284 1 9 SHEET 1 AA1 8 MET A 126 PHE A 127 0 SHEET 2 AA1 8 PHE A 285 GLU A 298 -1 O LEU A 296 N PHE A 127 SHEET 3 AA1 8 TYR A 305 PRO A 317 -1 O VAL A 314 N ALA A 289 SHEET 4 AA1 8 ARG A 235 VAL A 241 -1 N LEU A 240 O ALA A 311 SHEET 5 AA1 8 VAL A 205 LEU A 209 1 N CYS A 208 O ILE A 237 SHEET 6 AA1 8 THR A 146 LEU A 152 1 N LEU A 150 O SER A 207 SHEET 7 AA1 8 PHE A 167 THR A 173 1 O TYR A 171 N ASP A 151 SHEET 8 AA1 8 ARG A 189 VAL A 190 1 O ARG A 189 N ILE A 170 SHEET 1 AA2 2 VAL A 248 GLU A 249 0 SHEET 2 AA2 2 TRP A 255 GLU A 256 -1 O GLU A 256 N VAL A 248 SHEET 1 AA3 3 MET B 126 PHE B 127 0 SHEET 2 AA3 3 LEU B 296 GLU B 298 -1 O LEU B 296 N PHE B 127 SHEET 3 AA3 3 TYR B 305 TYR B 306 -1 O TYR B 306 N CYS B 297 SHEET 1 AA4 7 ARG B 189 VAL B 190 0 SHEET 2 AA4 7 PHE B 167 THR B 173 1 N ILE B 170 O ARG B 189 SHEET 3 AA4 7 THR B 146 LEU B 152 1 N HIS B 147 O GLU B 169 SHEET 4 AA4 7 VAL B 205 LEU B 209 1 O SER B 207 N LEU B 150 SHEET 5 AA4 7 ARG B 235 ALA B 239 1 O ILE B 237 N CYS B 208 SHEET 6 AA4 7 VAL B 312 PRO B 317 -1 O LEU B 315 N VAL B 236 SHEET 7 AA4 7 PHE B 285 THR B 291 -1 N ALA B 289 O VAL B 314 SHEET 1 AA5 2 VAL B 248 GLU B 249 0 SHEET 2 AA5 2 TRP B 255 GLU B 256 -1 O GLU B 256 N VAL B 248 CISPEP 1 LEU A 242 PRO A 243 0 10.26 CISPEP 2 LEU B 242 PRO B 243 0 -4.03 CRYST1 142.387 43.213 106.231 90.00 122.77 90.00 C 1 2 1 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 0.007023 0.000000 0.004521 0.00000 SCALE2 0.000000 0.023141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011195 0.00000