HEADER TRANSFERASE 09-JAN-26 10AX TITLE CRYSTAL STRUCTURE OF HUMAN SMYD1 IN COMPLEX WITH SINEFUNGIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SMYD1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SET AND MYND DOMAIN-CONTAINING PROTEIN 1; COMPND 5 EC: 2.1.1.354; COMPND 6 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: SMYD1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS METHYTRANSFERASE, SMYD1, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZENG,A.DONG,C.H.ARROWSMITH,A.M.EDWARDS,L.HALABELIAN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 1 02-SEP-26 10AX 0 JRNL AUTH H.ZENG,A.DONG,C.H.ARROWSMITH,A.M.EDWARDS,L.HALABELIAN, JRNL AUTH 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF HUMAN SMYD1 IN COMPLEX WITH SINEFUNGIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 808 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1152 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.4610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3511 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : 0.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.859 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.372 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.277 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 29.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.861 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3637 ; 0.005 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3321 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4916 ; 1.153 ; 1.828 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7599 ; 0.408 ; 1.754 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 448 ; 6.065 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 20 ; 5.413 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 582 ;15.343 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 534 ; 0.052 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4315 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 867 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1798 ; 1.233 ; 2.695 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1798 ; 1.232 ; 2.695 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2244 ; 2.185 ; 4.842 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2245 ; 2.184 ; 4.841 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1839 ; 1.228 ; 2.766 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1839 ; 1.228 ; 2.766 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2673 ; 2.125 ; 5.050 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4039 ; 3.702 ;25.100 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4040 ; 3.701 ;25.110 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 1004 REMARK 3 ORIGIN FOR THE GROUP (A): -48.3543 18.0425 -26.0536 REMARK 3 T TENSOR REMARK 3 T11: 0.0742 T22: 0.0183 REMARK 3 T33: 0.0618 T12: 0.0056 REMARK 3 T13: -0.0090 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 2.9302 L22: 0.7961 REMARK 3 L33: 0.3452 L12: 0.3775 REMARK 3 L13: 0.1207 L23: 0.2816 REMARK 3 S TENSOR REMARK 3 S11: -0.0150 S12: -0.1788 S13: 0.2632 REMARK 3 S21: -0.0689 S22: -0.0789 S23: 0.0387 REMARK 3 S31: 0.0292 S32: -0.0019 S33: 0.0939 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 10AX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1000304099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-24 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 : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.18049 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16731 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : 0.92900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24 % (W/V) PEG 4000, 20 % (V/V) REMARK 280 GLYCEROL, 0.16 M MAGNESIUM CHLORIDE, 0.08 M TRIS-HCL (PH 8.5), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 52.55400 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 103.31050 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 52.55400 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 103.31050 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 52.55400 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 103.31050 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 52.55400 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 103.31050 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 52.55400 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 103.31050 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 52.55400 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 103.31050 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 52.55400 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 103.31050 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 52.55400 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 52.55400 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 103.31050 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 -12 REMARK 465 GLY A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 LEU A 1 REMARK 465 VAL A 2 REMARK 465 PRO A 3 REMARK 465 ARG A 4 REMARK 465 ASN A 220 REMARK 465 HIS A 221 REMARK 465 GLU A 222 REMARK 465 ALA A 223 REMARK 465 VAL A 224 REMARK 465 LYS A 225 REMARK 465 SER A 226 REMARK 465 MET A 227 REMARK 465 PHE A 228 REMARK 465 HIS A 229 REMARK 465 GLU A 463 REMARK 465 ALA A 464 REMARK 465 ALA A 465 REMARK 465 LEU A 466 REMARK 465 ASN A 467 REMARK 465 ASN A 468 REMARK 465 GLN A 469 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 SER A 6 OG REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 GLU A 15 CG CD OE1 OE2 REMARK 470 ARG A 37 NE CZ NH1 NH2 REMARK 470 GLU A 60 CG CD OE1 OE2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LYS A 69 CD CE NZ REMARK 470 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 SER A 91 OG REMARK 470 LYS A 94 NZ REMARK 470 ARG A 95 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 98 NZ REMARK 470 LYS A 145 CD CE NZ REMARK 470 GLN A 168 CG CD OE1 NE2 REMARK 470 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 190 CG CD1 CD2 REMARK 470 GLN A 191 CG CD OE1 NE2 REMARK 470 THR A 230 OG1 CG2 REMARK 470 GLN A 231 CG CD OE1 NE2 REMARK 470 LYS A 267 NZ REMARK 470 GLN A 269 CD OE1 NE2 REMARK 470 ASP A 293 CG OD1 OD2 REMARK 470 ASN A 294 CG OD1 ND2 REMARK 470 LYS A 296 CD CE NZ REMARK 470 GLN A 299 CD OE1 NE2 REMARK 470 LYS A 303 CG CD CE NZ REMARK 470 GLU A 304 CG CD OE1 OE2 REMARK 470 LYS A 330 NZ REMARK 470 LYS A 338 CE NZ REMARK 470 LYS A 418 NZ REMARK 470 ARG A 449 CD NE CZ NH1 NH2 REMARK 470 TYR A 459 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 460 CG CD CE NZ REMARK 470 ARG A 462 CG CD NE CZ NH1 NH2 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 ALA A 30 -18.47 97.73 REMARK 500 HIS A 135 32.98 -93.81 REMARK 500 ARG A 188 36.38 -82.00 REMARK 500 TRP A 209 73.61 -119.04 REMARK 500 GLN A 231 -178.78 -172.98 REMARK 500 LYS A 284 -10.32 89.06 REMARK 500 LYS A 296 110.98 69.47 REMARK 500 VAL A 342 -60.61 -92.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 52 SG REMARK 620 2 CYS A 55 SG 111.6 REMARK 620 3 CYS A 74 SG 95.7 98.4 REMARK 620 4 CYS A 78 SG 104.3 125.1 118.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 CYS A 68 SG 106.4 REMARK 620 3 HIS A 86 NE2 121.2 102.6 REMARK 620 4 CYS A 90 SG 111.1 106.3 108.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 274 SG 113.1 REMARK 620 3 CYS A 276 SG 105.5 101.2 REMARK 620 4 CYS A 279 SG 114.6 110.8 110.6 REMARK 620 N 1 2 3 DBREF 10AX A 7 469 UNP Q8NB12 SMYD1_HUMAN 7 469 SEQADV 10AX MET A -12 UNP Q8NB12 INITIATING METHIONINE SEQADV 10AX GLY A -11 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX SER A -10 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX SER A -9 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX HIS A -8 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX HIS A -7 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX HIS A -6 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX HIS A -5 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX HIS A -4 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX HIS A -3 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX SER A -2 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX SER A -1 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX GLY A 0 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX LEU A 1 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX VAL A 2 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX PRO A 3 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX ARG A 4 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX GLY A 5 UNP Q8NB12 EXPRESSION TAG SEQADV 10AX SER A 6 UNP Q8NB12 EXPRESSION TAG SEQRES 1 A 482 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 482 LEU VAL PRO ARG GLY SER GLU ASN VAL GLU VAL PHE THR SEQRES 3 A 482 ALA GLU GLY LYS GLY ARG GLY LEU LYS ALA THR LYS GLU SEQRES 4 A 482 PHE TRP ALA ALA ASP ILE ILE PHE ALA GLU ARG ALA TYR SEQRES 5 A 482 SER ALA VAL VAL PHE ASP SER LEU VAL ASN PHE VAL CYS SEQRES 6 A 482 HIS THR CYS PHE LYS ARG GLN GLU LYS LEU HIS ARG CYS SEQRES 7 A 482 GLY GLN CYS LYS PHE ALA HIS TYR CYS ASP ARG THR CYS SEQRES 8 A 482 GLN LYS ASP ALA TRP LEU ASN HIS LYS ASN GLU CYS SER SEQRES 9 A 482 ALA ILE LYS ARG TYR GLY LYS VAL PRO ASN GLU ASN ILE SEQRES 10 A 482 ARG LEU ALA ALA ARG ILE MET TRP ARG VAL GLU ARG GLU SEQRES 11 A 482 GLY THR GLY LEU THR GLU GLY CYS LEU VAL SER VAL ASP SEQRES 12 A 482 ASP LEU GLN ASN HIS VAL GLU HIS PHE GLY GLU GLU GLU SEQRES 13 A 482 GLN LYS ASP LEU ARG VAL ASP VAL ASP THR PHE LEU GLN SEQRES 14 A 482 TYR TRP PRO PRO GLN SER GLN GLN PHE SER MET GLN TYR SEQRES 15 A 482 ILE SER HIS ILE PHE GLY VAL ILE ASN CYS ASN GLY PHE SEQRES 16 A 482 THR LEU SER ASP GLN ARG GLY LEU GLN ALA VAL GLY VAL SEQRES 17 A 482 GLY ILE PHE PRO ASN LEU GLY LEU VAL ASN HIS ASP CYS SEQRES 18 A 482 TRP PRO ASN CYS THR VAL ILE PHE ASN ASN GLY ASN HIS SEQRES 19 A 482 GLU ALA VAL LYS SER MET PHE HIS THR GLN MET ARG ILE SEQRES 20 A 482 GLU LEU ARG ALA LEU GLY LYS ILE SER GLU GLY GLU GLU SEQRES 21 A 482 LEU THR VAL SER TYR ILE ASP PHE LEU ASN VAL SER GLU SEQRES 22 A 482 GLU ARG LYS ARG GLN LEU LYS LYS GLN TYR TYR PHE ASP SEQRES 23 A 482 CYS THR CYS GLU HIS CYS GLN LYS LYS LEU LYS ASP ASP SEQRES 24 A 482 LEU PHE LEU GLY VAL LYS ASP ASN PRO LYS PRO SER GLN SEQRES 25 A 482 GLU VAL VAL LYS GLU MET ILE GLN PHE SER LYS ASP THR SEQRES 26 A 482 LEU GLU LYS ILE ASP LYS ALA ARG SER GLU GLY LEU TYR SEQRES 27 A 482 HIS GLU VAL VAL LYS LEU CYS ARG GLU CYS LEU GLU LYS SEQRES 28 A 482 GLN GLU PRO VAL PHE ALA ASP THR ASN ILE TYR MET LEU SEQRES 29 A 482 ARG MET LEU SER ILE VAL SER GLU VAL LEU SER TYR LEU SEQRES 30 A 482 GLN ALA PHE GLU GLU ALA SER PHE TYR ALA ARG ARG MET SEQRES 31 A 482 VAL ASP GLY TYR MET LYS LEU TYR HIS PRO ASN ASN ALA SEQRES 32 A 482 GLN LEU GLY MET ALA VAL MET ARG ALA GLY LEU THR ASN SEQRES 33 A 482 TRP HIS ALA GLY ASN ILE GLU VAL GLY HIS GLY MET ILE SEQRES 34 A 482 CYS LYS ALA TYR ALA ILE LEU LEU VAL THR HIS GLY PRO SEQRES 35 A 482 SER HIS PRO ILE THR LYS ASP LEU GLU ALA MET ARG VAL SEQRES 36 A 482 GLN THR GLU MET GLU LEU ARG MET PHE ARG GLN ASN GLU SEQRES 37 A 482 PHE MET TYR TYR LYS MET ARG GLU ALA ALA LEU ASN ASN SEQRES 38 A 482 GLN HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET SFG A1004 27 HET UNX A1005 1 HETNAM ZN ZINC ION HETNAM SFG SINEFUNGIN HETNAM UNX UNKNOWN ATOM OR ION HETSYN SFG ADENOSYL-ORNITHINE FORMUL 2 ZN 3(ZN 2+) FORMUL 5 SFG C15 H23 N7 O5 FORMUL 6 UNX X FORMUL 7 HOH *21(H2 O) HELIX 1 AA1 GLY A 5 GLU A 7 5 3 HELIX 2 AA2 ASP A 45 VAL A 48 5 4 HELIX 3 AA3 ASP A 75 GLY A 97 1 23 HELIX 4 AA4 ASN A 101 GLY A 118 1 18 HELIX 5 AA5 SER A 128 LEU A 132 5 5 HELIX 6 AA6 HIS A 135 PHE A 139 5 5 HELIX 7 AA7 GLY A 140 TRP A 158 1 19 HELIX 8 AA8 SER A 166 ASN A 180 1 15 HELIX 9 AA9 ASN A 200 VAL A 204 5 5 HELIX 10 AB1 VAL A 258 TYR A 271 1 14 HELIX 11 AB2 CYS A 276 LYS A 281 1 6 HELIX 12 AB3 LYS A 284 LEU A 289 1 6 HELIX 13 AB4 SER A 298 GLU A 322 1 25 HELIX 14 AB5 LEU A 324 GLU A 340 1 17 HELIX 15 AB6 ASN A 347 LEU A 364 1 18 HELIX 16 AB7 ALA A 366 TYR A 385 1 20 HELIX 17 AB8 ASN A 389 GLY A 407 1 19 HELIX 18 AB9 ASN A 408 HIS A 427 1 20 HELIX 19 AC1 HIS A 431 ARG A 462 1 32 SHEET 1 AA1 4 VAL A 9 ALA A 14 0 SHEET 2 AA1 4 GLY A 18 ALA A 23 -1 O LYS A 22 N GLU A 10 SHEET 3 AA1 4 GLU A 247 VAL A 250 -1 O LEU A 248 N LEU A 21 SHEET 4 AA1 4 ASN A 205 HIS A 206 1 N ASN A 205 O VAL A 250 SHEET 1 AA2 3 ILE A 32 GLU A 36 0 SHEET 2 AA2 3 ARG A 233 ALA A 238 -1 O LEU A 236 N ILE A 33 SHEET 3 AA2 3 CYS A 212 ASN A 217 -1 N ASN A 217 O ARG A 233 SHEET 1 AA3 3 SER A 40 VAL A 43 0 SHEET 2 AA3 3 ALA A 192 ILE A 197 -1 O VAL A 195 N VAL A 42 SHEET 3 AA3 3 GLY A 181 SER A 185 -1 N LEU A 184 O GLY A 194 SHEET 1 AA4 2 HIS A 63 ARG A 64 0 SHEET 2 AA4 2 HIS A 72 TYR A 73 -1 O TYR A 73 N HIS A 63 LINK SG CYS A 52 ZN ZN A1002 1555 1555 2.30 LINK SG CYS A 55 ZN ZN A1002 1555 1555 2.27 LINK SG CYS A 65 ZN ZN A1003 1555 1555 2.30 LINK SG CYS A 68 ZN ZN A1003 1555 1555 2.32 LINK SG CYS A 74 ZN ZN A1002 1555 1555 2.33 LINK SG CYS A 78 ZN ZN A1002 1555 1555 2.32 LINK NE2 HIS A 86 ZN ZN A1003 1555 1555 2.08 LINK SG CYS A 90 ZN ZN A1003 1555 1555 2.30 LINK SG CYS A 208 ZN ZN A1001 1555 1555 2.32 LINK SG CYS A 274 ZN ZN A1001 1555 1555 2.31 LINK SG CYS A 276 ZN ZN A1001 1555 1555 2.32 LINK SG CYS A 279 ZN ZN A1001 1555 1555 2.33 CRYST1 105.108 105.108 206.621 90.00 90.00 90.00 I 4 2 2 16 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 0.009514 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004840 0.00000 CONECT 357 3523 CONECT 380 3523 CONECT 465 3524 CONECT 484 3524 CONECT 534 3523 CONECT 560 3523 CONECT 627 3524 CONECT 659 3524 CONECT 1572 3522 CONECT 2030 3522 CONECT 2043 3522 CONECT 2068 3522 CONECT 3522 1572 2030 2043 2068 CONECT 3523 357 380 534 560 CONECT 3524 465 484 627 659 CONECT 3525 3526 CONECT 3526 3525 3527 3530 CONECT 3527 3526 3528 3529 CONECT 3528 3527 CONECT 3529 3527 CONECT 3530 3526 3531 CONECT 3531 3530 3532 CONECT 3532 3531 3533 3534 CONECT 3533 3532 CONECT 3534 3532 3535 CONECT 3535 3534 3536 3537 CONECT 3536 3535 3541 CONECT 3537 3535 3538 3539 CONECT 3538 3537 CONECT 3539 3537 3540 3541 CONECT 3540 3539 CONECT 3541 3536 3539 3542 CONECT 3542 3541 3543 3551 CONECT 3543 3542 3544 CONECT 3544 3543 3545 CONECT 3545 3544 3546 3551 CONECT 3546 3545 3547 3548 CONECT 3547 3546 CONECT 3548 3546 3549 CONECT 3549 3548 3550 CONECT 3550 3549 3551 CONECT 3551 3542 3545 3550 MASTER 439 0 5 19 12 0 0 6 3563 1 42 38 END