HEADER TRANSFERASE 22-DEC-21 7QNU TITLE SMYD3 IN COMPLEX WITH FRAGMENT FL08619 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SET AND MYND DOMAIN-CONTAINING PROTEIN 3,ZINC FINGER MYND COMPND 5 DOMAIN-CONTAINING PROTEIN 1; COMPND 6 EC: 2.1.1.354; 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: SMYD3, ZMYND1, ZNFN3A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS METHYLTRANSFERASE, EPIGENETIC, ONCOGEN, HISTONE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.A.LUND,D.CEDERFELT,D.DOBRITZSCH REVDAT 3 24-APR-24 7QNU 1 JRNL REVDAT 2 07-FEB-24 7QNU 1 REMARK REVDAT 1 05-APR-23 7QNU 0 JRNL AUTH E.A.FITZGERALD,D.CEDERFELT,B.A.LUND,N.MYERS,H.ZHANG, JRNL AUTH 2 D.DOBRITZSCH,H.DANIELSON JRNL TITL IDENTIFICATION OF FRAGMENTS TARGETING SMYD3 USING HIGHLY JRNL TITL 2 SENSITIVE KINETIC AND MULTIPLEXED BIOSENSOR-BASED SCREENING JRNL REF RSC MED CHEM 2024 JRNL REFN ESSN 2632-8682 JRNL DOI 10.1039/D4MD00093E REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC4_4425 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.2 REMARK 3 NUMBER OF REFLECTIONS : 38744 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1987 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 41.0800 - 3.9400 0.99 3753 199 0.1842 0.2013 REMARK 3 2 3.9400 - 3.1300 0.99 3580 188 0.1588 0.1996 REMARK 3 3 3.1300 - 2.7300 1.00 3550 202 0.1719 0.2265 REMARK 3 4 2.7300 - 2.4800 1.00 3543 192 0.1811 0.2381 REMARK 3 5 2.4800 - 2.3000 1.00 3523 199 0.1739 0.2118 REMARK 3 6 2.3000 - 2.1700 1.00 3528 186 0.1799 0.2316 REMARK 3 7 2.1700 - 2.0600 0.96 3353 169 0.1850 0.2957 REMARK 3 8 2.0600 - 1.9700 0.90 3168 174 0.2070 0.2393 REMARK 3 9 1.9700 - 1.8900 0.84 2921 161 0.2313 0.2845 REMARK 3 10 1.8900 - 1.8300 0.72 2524 129 0.2401 0.2957 REMARK 3 11 1.8300 - 1.7700 0.59 2045 113 0.2615 0.3063 REMARK 3 12 1.7700 - 1.7200 0.27 941 52 0.2686 0.3383 REMARK 3 13 1.7200 - 1.6800 0.08 281 19 0.2856 0.2831 REMARK 3 14 1.6800 - 1.6400 0.01 47 4 0.3121 0.3474 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) : 0.173 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.669 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.61 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 : 0.009 3550 REMARK 3 ANGLE : 0.874 4791 REMARK 3 CHIRALITY : 0.050 526 REMARK 3 PLANARITY : 0.012 625 REMARK 3 DIHEDRAL : 21.787 499 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|3 - 40} REMARK 3 ORIGIN FOR THE GROUP (A): 3.4154 5.5741 21.4704 REMARK 3 T TENSOR REMARK 3 T11: 0.0870 T22: 0.1203 REMARK 3 T33: 0.1417 T12: 0.0120 REMARK 3 T13: -0.0376 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 0.5824 L22: 1.8234 REMARK 3 L33: 2.6900 L12: -0.3900 REMARK 3 L13: -0.6485 L23: -0.0262 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: -0.0765 S13: -0.0699 REMARK 3 S21: 0.0570 S22: 0.0860 S23: 0.2882 REMARK 3 S31: 0.0840 S32: -0.1324 S33: -0.0560 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|41 - 72} REMARK 3 ORIGIN FOR THE GROUP (A): 15.6290 -2.0434 -6.0260 REMARK 3 T TENSOR REMARK 3 T11: 0.2485 T22: 0.1200 REMARK 3 T33: 0.1522 T12: 0.0598 REMARK 3 T13: -0.0186 T23: -0.0449 REMARK 3 L TENSOR REMARK 3 L11: 2.4151 L22: 3.1011 REMARK 3 L33: 2.1981 L12: 0.6414 REMARK 3 L13: 0.1251 L23: 1.1536 REMARK 3 S TENSOR REMARK 3 S11: 0.1135 S12: 0.2315 S13: -0.2437 REMARK 3 S21: -0.2629 S22: 0.0004 S23: -0.3079 REMARK 3 S31: 0.2370 S32: 0.2837 S33: -0.0867 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|73 - 92} REMARK 3 ORIGIN FOR THE GROUP (A): 8.2691 6.2745 -8.3652 REMARK 3 T TENSOR REMARK 3 T11: 0.2366 T22: 0.1323 REMARK 3 T33: 0.1602 T12: -0.0135 REMARK 3 T13: -0.0491 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 2.5602 L22: 7.9499 REMARK 3 L33: 1.4264 L12: 1.1659 REMARK 3 L13: 1.1951 L23: 1.6096 REMARK 3 S TENSOR REMARK 3 S11: -0.0973 S12: 0.1385 S13: 0.2915 REMARK 3 S21: -0.5997 S22: 0.1938 S23: 0.5322 REMARK 3 S31: 0.0943 S32: -0.0067 S33: -0.1067 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|93 - 155} REMARK 3 ORIGIN FOR THE GROUP (A): 14.1661 16.9078 5.2127 REMARK 3 T TENSOR REMARK 3 T11: 0.1000 T22: 0.0608 REMARK 3 T33: 0.0829 T12: 0.0034 REMARK 3 T13: -0.0233 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 1.8880 L22: 1.5668 REMARK 3 L33: 1.9612 L12: 0.3787 REMARK 3 L13: 0.0281 L23: 0.3347 REMARK 3 S TENSOR REMARK 3 S11: -0.0759 S12: 0.0867 S13: -0.0089 REMARK 3 S21: -0.1852 S22: 0.0917 S23: -0.0226 REMARK 3 S31: -0.0529 S32: 0.0680 S33: -0.0102 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {A|156 - 225} REMARK 3 ORIGIN FOR THE GROUP (A): 11.6389 8.8957 10.4657 REMARK 3 T TENSOR REMARK 3 T11: 0.0874 T22: 0.0929 REMARK 3 T33: 0.0785 T12: 0.0138 REMARK 3 T13: -0.0349 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.8655 L22: 1.4736 REMARK 3 L33: 1.1236 L12: -0.0165 REMARK 3 L13: 0.0993 L23: -0.2186 REMARK 3 S TENSOR REMARK 3 S11: 0.0390 S12: 0.0266 S13: -0.0225 REMARK 3 S21: -0.1265 S22: 0.0015 S23: 0.0485 REMARK 3 S31: 0.0813 S32: -0.0195 S33: -0.0354 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {A|226 - 366} REMARK 3 ORIGIN FOR THE GROUP (A): 28.1306 -4.3293 19.9009 REMARK 3 T TENSOR REMARK 3 T11: 0.1092 T22: 0.1099 REMARK 3 T33: 0.0961 T12: 0.0055 REMARK 3 T13: -0.0405 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.7400 L22: 1.1516 REMARK 3 L33: 0.4549 L12: -0.4407 REMARK 3 L13: -0.2374 L23: -0.1047 REMARK 3 S TENSOR REMARK 3 S11: -0.0278 S12: -0.0676 S13: 0.0631 REMARK 3 S21: -0.0042 S22: 0.0372 S23: -0.0893 REMARK 3 S31: 0.0439 S32: 0.0449 S33: -0.0129 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: {A|367 - 428} REMARK 3 ORIGIN FOR THE GROUP (A): 12.9686 -21.1288 16.7885 REMARK 3 T TENSOR REMARK 3 T11: 0.1574 T22: 0.0897 REMARK 3 T33: 0.2005 T12: 0.0014 REMARK 3 T13: -0.0699 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.3898 L22: 3.6026 REMARK 3 L33: 0.8859 L12: -0.0251 REMARK 3 L13: -0.1865 L23: 0.4678 REMARK 3 S TENSOR REMARK 3 S11: 0.0329 S12: -0.0124 S13: -0.3556 REMARK 3 S21: -0.1828 S22: 0.0169 S23: 0.2598 REMARK 3 S31: 0.1113 S32: -0.0226 S33: -0.0173 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 7QNU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.25-8.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976256 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 : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48981 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 41.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.21420 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 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: 6Z2R REMARK 200 REMARK 200 REMARK: NEEDLE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.25-8.75 0.1M MAGNESIUM REMARK 280 ACETATE 15-18 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 29.96550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.54250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.94300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.54250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.96550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.94300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 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 HZ2 LYS A 284 O HOH A 625 1.58 REMARK 500 HE ARG A 25 O HOH A 624 1.58 REMARK 500 O HOH A 813 O HOH A 897 1.94 REMARK 500 OD2 ASP A 398 O HOH A 601 1.98 REMARK 500 O HOH A 616 O HOH A 674 1.99 REMARK 500 O PRO A 167 O HOH A 602 2.02 REMARK 500 O HOH A 603 O HOH A 637 2.03 REMARK 500 O HOH A 603 O HOH A 763 2.04 REMARK 500 O HOH A 854 O HOH A 879 2.05 REMARK 500 O HOH A 642 O HOH A 722 2.06 REMARK 500 OE1 GLN A 372 O HOH A 603 2.07 REMARK 500 OD1 ASP A 332 O HOH A 603 2.10 REMARK 500 O HOH A 603 O HOH A 716 2.10 REMARK 500 O HOH A 684 O HOH A 930 2.15 REMARK 500 O HOH A 986 O HOH A 1019 2.15 REMARK 500 O HOH A 716 O HOH A 858 2.15 REMARK 500 O HOH A 956 O HOH A 1003 2.17 REMARK 500 O HOH A 992 O HOH A 1017 2.18 REMARK 500 O HOH A 714 O HOH A 894 2.19 REMARK 500 O HOH A 704 O HOH A 898 2.19 REMARK 500 O HOH A 885 O HOH A 988 2.19 REMARK 500 O HOH A 601 O HOH A 630 2.19 REMARK 500 OE1 GLN A 191 O HOH A 604 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 834 O HOH A 950 3645 2.02 REMARK 500 O HOH A 964 O HOH A 1000 3645 2.08 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 ASN A 13 20.16 -147.21 REMARK 500 ARG A 51 -62.75 -90.75 REMARK 500 ARG A 66 16.24 57.22 REMARK 500 LYS A 94 -63.84 -28.08 REMARK 500 TYR A 124 130.12 -173.88 REMARK 500 LYS A 271 -4.00 80.13 REMARK 500 LEU A 343 77.90 -100.32 REMARK 500 ALA A 427 7.26 -66.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 406 0.12 SIDE CHAIN 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 A1045 DISTANCE = 6.79 ANGSTROMS 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 A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 104.1 REMARK 620 3 CYS A 71 SG 112.5 110.8 REMARK 620 4 CYS A 75 SG 111.0 118.0 100.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 CYS A 65 SG 113.8 REMARK 620 3 HIS A 83 NE2 109.7 105.4 REMARK 620 4 CYS A 87 SG 108.6 112.1 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 112.3 REMARK 620 3 CYS A 263 SG 105.8 109.1 REMARK 620 4 CYS A 266 SG 99.8 117.4 111.7 REMARK 620 N 1 2 3 DBREF 7QNU A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 7QNU GLY A -2 UNP Q9H7B4 EXPRESSION TAG SEQADV 7QNU SER A -1 UNP Q9H7B4 EXPRESSION TAG SEQADV 7QNU HIS A 0 UNP Q9H7B4 EXPRESSION TAG SEQADV 7QNU ASN A 13 UNP Q9H7B4 LYS 13 ENGINEERED MUTATION SEQADV 7QNU ARG A 140 UNP Q9H7B4 LYS 140 ENGINEERED MUTATION SEQRES 1 A 431 GLY SER HIS MET GLU PRO LEU LYS VAL GLU LYS PHE ALA SEQRES 2 A 431 THR ALA ASN ARG GLY ASN GLY LEU ARG ALA VAL THR PRO SEQRES 3 A 431 LEU ARG PRO GLY GLU LEU LEU PHE ARG SER ASP PRO LEU SEQRES 4 A 431 ALA TYR THR VAL CYS LYS GLY SER ARG GLY VAL VAL CYS SEQRES 5 A 431 ASP ARG CYS LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SEQRES 6 A 431 SER GLN CYS ARG VAL ALA LYS TYR CYS SER ALA LYS CYS SEQRES 7 A 431 GLN LYS LYS ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS SEQRES 8 A 431 CYS LEU LYS SER CYS LYS PRO ARG TYR PRO PRO ASP SER SEQRES 9 A 431 VAL ARG LEU LEU GLY ARG VAL VAL PHE LYS LEU MET ASP SEQRES 10 A 431 GLY ALA PRO SER GLU SER GLU LYS LEU TYR SER PHE TYR SEQRES 11 A 431 ASP LEU GLU SER ASN ILE ASN LYS LEU THR GLU ASP ARG SEQRES 12 A 431 LYS GLU GLY LEU ARG GLN LEU VAL MET THR PHE GLN HIS SEQRES 13 A 431 PHE MET ARG GLU GLU ILE GLN ASP ALA SER GLN LEU PRO SEQRES 14 A 431 PRO ALA PHE ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE SEQRES 15 A 431 CYS ASN SER PHE THR ILE CYS ASN ALA GLU MET GLN GLU SEQRES 16 A 431 VAL GLY VAL GLY LEU TYR PRO SER ILE SER LEU LEU ASN SEQRES 17 A 431 HIS SER CYS ASP PRO ASN CYS SER ILE VAL PHE ASN GLY SEQRES 18 A 431 PRO HIS LEU LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL SEQRES 19 A 431 GLY GLU GLU LEU THR ILE CYS TYR LEU ASP MET LEU MET SEQRES 20 A 431 THR SER GLU GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR SEQRES 21 A 431 CYS PHE GLU CYS ASP CYS PHE ARG CYS GLN THR GLN ASP SEQRES 22 A 431 LYS ASP ALA ASP MET LEU THR GLY ASP GLU GLN VAL TRP SEQRES 23 A 431 LYS GLU VAL GLN GLU SER LEU LYS LYS ILE GLU GLU LEU SEQRES 24 A 431 LYS ALA HIS TRP LYS TRP GLU GLN VAL LEU ALA MET CYS SEQRES 25 A 431 GLN ALA ILE ILE SER SER ASN SER GLU ARG LEU PRO ASP SEQRES 26 A 431 ILE ASN ILE TYR GLN LEU LYS VAL LEU ASP CYS ALA MET SEQRES 27 A 431 ASP ALA CYS ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU SEQRES 28 A 431 PHE TYR GLY THR ARG THR MET GLU PRO TYR ARG ILE PHE SEQRES 29 A 431 PHE PRO GLY SER HIS PRO VAL ARG GLY VAL GLN VAL MET SEQRES 30 A 431 LYS VAL GLY LYS LEU GLN LEU HIS GLN GLY MET PHE PRO SEQRES 31 A 431 GLN ALA MET LYS ASN LEU ARG LEU ALA PHE ASP ILE MET SEQRES 32 A 431 ARG VAL THR HIS GLY ARG GLU HIS SER LEU ILE GLU ASP SEQRES 33 A 431 LEU ILE LEU LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG SEQRES 34 A 431 ALA SER HET SAM A 501 46 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET 173 A 505 17 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM ZN ZINC ION HETNAM 173 BENZOYL-FORMIC ACID HETSYN 173 OXO(PHENYL)ACETIC ACID FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 ZN 3(ZN 2+) FORMUL 6 173 C8 H6 O3 FORMUL 7 HOH *445(H2 O) HELIX 1 AA1 LYS A 42 ARG A 45 5 4 HELIX 2 AA2 SER A 72 CYS A 93 1 22 HELIX 3 AA3 PRO A 99 GLY A 115 1 17 HELIX 4 AA4 SER A 118 LYS A 122 5 5 HELIX 5 AA5 SER A 125 LEU A 129 5 5 HELIX 6 AA6 ASN A 132 LEU A 136 5 5 HELIX 7 AA7 THR A 137 ARG A 156 1 20 HELIX 8 AA8 ASP A 161 LEU A 165 5 5 HELIX 9 AA9 ASP A 170 SER A 182 1 13 HELIX 10 AB1 SER A 200 LEU A 204 5 5 HELIX 11 AB2 THR A 245 CYS A 258 1 14 HELIX 12 AB3 CYS A 263 GLN A 269 1 7 HELIX 13 AB4 LYS A 271 LEU A 276 1 6 HELIX 14 AB5 ASP A 279 HIS A 299 1 21 HELIX 15 AB6 LYS A 301 SER A 314 1 14 HELIX 16 AB7 ASN A 324 GLY A 342 1 19 HELIX 17 AB8 LEU A 343 PHE A 362 1 20 HELIX 18 AB9 HIS A 366 GLN A 383 1 18 HELIX 19 AC1 MET A 385 HIS A 404 1 20 HELIX 20 AC2 HIS A 408 ALA A 427 1 20 SHEET 1 AA1 4 VAL A 6 ALA A 10 0 SHEET 2 AA1 4 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9 SHEET 3 AA1 4 GLU A 234 ILE A 237 -1 O LEU A 235 N LEU A 18 SHEET 4 AA1 4 ASN A 205 HIS A 206 1 N ASN A 205 O ILE A 237 SHEET 1 AA2 3 LEU A 29 SER A 33 0 SHEET 2 AA2 3 HIS A 220 ALA A 225 -1 O LEU A 223 N LEU A 30 SHEET 3 AA2 3 CYS A 212 ASN A 217 -1 N ASN A 217 O HIS A 220 SHEET 1 AA3 3 ALA A 37 VAL A 40 0 SHEET 2 AA3 3 GLU A 192 LEU A 197 -1 O LEU A 197 N ALA A 37 SHEET 3 AA3 3 PHE A 183 CYS A 186 -1 N PHE A 183 O GLY A 196 SHEET 1 AA4 2 MET A 60 ARG A 61 0 SHEET 2 AA4 2 LYS A 69 TYR A 70 -1 O TYR A 70 N MET A 60 LINK SG CYS A 49 ZN ZN A 503 1555 1555 2.28 LINK SG CYS A 52 ZN ZN A 503 1555 1555 2.32 LINK SG CYS A 62 ZN ZN A 504 1555 1555 2.38 LINK SG CYS A 65 ZN ZN A 504 1555 1555 2.22 LINK SG CYS A 71 ZN ZN A 503 1555 1555 2.27 LINK SG CYS A 75 ZN ZN A 503 1555 1555 2.16 LINK NE2 HIS A 83 ZN ZN A 504 1555 1555 2.01 LINK SG CYS A 87 ZN ZN A 504 1555 1555 2.23 LINK SG CYS A 208 ZN ZN A 502 1555 1555 2.28 LINK SG CYS A 261 ZN ZN A 502 1555 1555 2.34 LINK SG CYS A 263 ZN ZN A 502 1555 1555 2.24 LINK SG CYS A 266 ZN ZN A 502 1555 1555 2.34 CRYST1 59.931 65.886 105.085 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 0.016686 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009516 0.00000