HEADER TRANSFERASE 21-DEC-12 4IJ8 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF SETD8 WITH SAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-LYSINE METHYLTRANSFERASE SETD8; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: H4-K20-HMTASE SETD8, HISTONE-LYSINE N-METHYLTRANSFERASE COMPND 5 SETD8, LYSINE N-METHYLTRANSFERASE 5A, PR/SET DOMAIN-CONTAINING COMPND 6 PROTEIN 07, PR-SET7, PR/SET07, SET DOMAIN-CONTAINING PROTEIN 8; COMPND 7 EC: 2.1.1.-, 2.1.1.43; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HELICAL PEPTIDE; COMPND 12 CHAIN: I; COMPND 13 FRAGMENT: SEE REMARK 999; COMPND 14 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: SETD8, KMT5A, PRSET7, SET07, SET8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHIS2; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 12 ORGANISM_TAXID: 32644; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, N-LYSINE METHYLTRANSFERASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.YU,W.TEMPEL,Y.LI,M.EL BAKKOURI,M.SHAPIRA,C.BOUNTRA,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,P.J.BROWN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 20-SEP-23 4IJ8 1 REMARK SEQADV REVDAT 2 02-APR-14 4IJ8 1 SOURCE REVDAT 1 16-JAN-13 4IJ8 0 JRNL AUTH W.YU,W.TEMPEL,Y.LI,M.EL BAKKOURI,M.SHAPIRA,C.BOUNTRA, JRNL AUTH 2 C.H.ARROWSMITH,A.M.EDWARDS,P.J.BROWN, JRNL AUTH 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF SETD8 WITH SAM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29561 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1516 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2116 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 2 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2440 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.44000 REMARK 3 B12 (A**2) : -0.14000 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): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.332 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2575 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2342 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3497 ; 1.481 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5383 ; 0.720 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 6.144 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;30.140 ;24.107 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 418 ;11.840 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.086 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 391 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2945 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 583 ; 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): 1303 ; 1.645 ; 2.224 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1302 ; 1.645 ; 2.223 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1624 ; 2.380 ; 3.323 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 233 A 393 REMARK 3 ORIGIN FOR THE GROUP (A): -11.2089 34.0938 4.9505 REMARK 3 T TENSOR REMARK 3 T11: 0.0592 T22: 0.0553 REMARK 3 T33: 0.1252 T12: -0.0157 REMARK 3 T13: 0.0447 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 2.3918 L22: 1.4072 REMARK 3 L33: 1.7877 L12: 0.0310 REMARK 3 L13: -0.1607 L23: 0.4080 REMARK 3 S TENSOR REMARK 3 S11: -0.0796 S12: 0.0487 S13: 0.0541 REMARK 3 S21: -0.0558 S22: 0.0252 S23: -0.3596 REMARK 3 S31: 0.0240 S32: 0.2652 S33: 0.0544 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 244 B 393 REMARK 3 ORIGIN FOR THE GROUP (A): -37.9893 20.1746 3.5645 REMARK 3 T TENSOR REMARK 3 T11: 0.1112 T22: 0.0561 REMARK 3 T33: 0.1106 T12: -0.0592 REMARK 3 T13: 0.0349 T23: -0.0603 REMARK 3 L TENSOR REMARK 3 L11: 2.8454 L22: 2.2859 REMARK 3 L33: 1.7569 L12: -0.2796 REMARK 3 L13: -0.1013 L23: -0.1508 REMARK 3 S TENSOR REMARK 3 S11: -0.0104 S12: 0.1036 S13: -0.4324 REMARK 3 S21: -0.1415 S22: -0.1416 S23: 0.2694 REMARK 3 S31: 0.3434 S32: -0.1925 S33: 0.1520 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : WITH TLS ADDED REMARK 3 ARP/WARP, COOT, AND THE MOLPROBITY SERVER WERE ALSO USED DURING REMARK 3 REFINEMENT. REMARK 4 REMARK 4 4IJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076820. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29619 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 87.849 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11200 REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.00 REMARK 200 R MERGE FOR SHELL (I) : 0.94200 REMARK 200 R SYM FOR SHELL (I) : 0.94200 REMARK 200 FOR SHELL : 0.800 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: PDB ENTRY 1ZKK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM CITRATE, 0.1 M HEPES, 10 REMARK 280 -FOLD EXCESS SAM, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.93300 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 93.86600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 70.39950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.33250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.46650 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.93300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 93.86600 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 117.33250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 70.39950 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 23.46650 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 658 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 631 LIES ON A SPECIAL POSITION. 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 ALA A 229 REMARK 465 MET A 230 REMARK 465 GLY A 231 REMARK 465 SER A 232 REMARK 465 ALA B 229 REMARK 465 MET B 230 REMARK 465 GLY B 231 REMARK 465 SER B 232 REMARK 465 ARG B 233 REMARK 465 LYS B 234 REMARK 465 SER B 235 REMARK 465 LYS B 236 REMARK 465 ALA B 237 REMARK 465 GLU B 238 REMARK 465 LEU B 239 REMARK 465 GLN B 240 REMARK 465 SER B 241 REMARK 465 GLU B 242 REMARK 465 GLU B 243 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 ARG A 233 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 234 CE NZ REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 LEU A 239 CG CD1 CD2 REMARK 470 GLN A 240 CG CD OE1 NE2 REMARK 470 SER A 241 OG REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 GLU A 243 CG CD OE1 OE2 REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 ARG A 246 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 247 CD1 REMARK 470 GLU A 249 CG CD OE1 OE2 REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 GLU A 257 CD OE1 OE2 REMARK 470 ARG A 279 NE CZ NH1 NH2 REMARK 470 LYS A 297 CD CE NZ REMARK 470 LYS A 382 CD CE NZ REMARK 470 ARG B 244 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 245 CG CD CE NZ REMARK 470 ARG B 246 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 247 CD1 REMARK 470 GLU B 249 CG CD OE1 OE2 REMARK 470 LYS B 260 NZ REMARK 470 ARG B 279 NH1 NH2 REMARK 470 LYS B 297 CG CD CE NZ REMARK 470 ARG B 329 CD NE CZ NH1 NH2 REMARK 470 LYS B 349 CD CE NZ REMARK 470 ASP B 354 CG OD1 OD2 REMARK 470 LYS B 382 NZ 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 O MET A 313 UNK UNX A 502 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 299 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 VAL A 283 -61.79 -102.36 REMARK 500 LEU A 319 -125.56 52.28 REMARK 500 LEU B 319 -121.76 55.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM B 501 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MODEL INCLUDES A DISJOINT APPARENT ALPHA-HELIX THAT COULD NOT REMARK 999 BE ASSIGNED TO A SPECIFIC SECTION OF THE AMINO ACID SEQUENCE OF THE REMARK 999 TARGET PROTEIN. DBREF 4IJ8 A 232 393 UNP Q9NQR1 SETD8_HUMAN 232 393 DBREF 4IJ8 B 232 393 UNP Q9NQR1 SETD8_HUMAN 232 393 DBREF 4IJ8 I 4 13 PDB 4IJ8 4IJ8 4 13 SEQADV 4IJ8 ALA A 229 UNP Q9NQR1 EXPRESSION TAG SEQADV 4IJ8 MET A 230 UNP Q9NQR1 EXPRESSION TAG SEQADV 4IJ8 GLY A 231 UNP Q9NQR1 EXPRESSION TAG SEQADV 4IJ8 SER A 343 UNP Q9NQR1 CYS 343 ENGINEERED MUTATION SEQADV 4IJ8 ALA B 229 UNP Q9NQR1 EXPRESSION TAG SEQADV 4IJ8 MET B 230 UNP Q9NQR1 EXPRESSION TAG SEQADV 4IJ8 GLY B 231 UNP Q9NQR1 EXPRESSION TAG SEQADV 4IJ8 SER B 343 UNP Q9NQR1 CYS 343 ENGINEERED MUTATION SEQRES 1 A 165 ALA MET GLY SER ARG LYS SER LYS ALA GLU LEU GLN SER SEQRES 2 A 165 GLU GLU ARG LYS ARG ILE ASP GLU LEU ILE GLU SER GLY SEQRES 3 A 165 LYS GLU GLU GLY MET LYS ILE ASP LEU ILE ASP GLY LYS SEQRES 4 A 165 GLY ARG GLY VAL ILE ALA THR LYS GLN PHE SER ARG GLY SEQRES 5 A 165 ASP PHE VAL VAL GLU TYR HIS GLY ASP LEU ILE GLU ILE SEQRES 6 A 165 THR ASP ALA LYS LYS ARG GLU ALA LEU TYR ALA GLN ASP SEQRES 7 A 165 PRO SER THR GLY CYS TYR MET TYR TYR PHE GLN TYR LEU SEQRES 8 A 165 SER LYS THR TYR CYS VAL ASP ALA THR ARG GLU THR ASN SEQRES 9 A 165 ARG LEU GLY ARG LEU ILE ASN HIS SER LYS SER GLY ASN SEQRES 10 A 165 CYS GLN THR LYS LEU HIS ASP ILE ASP GLY VAL PRO HIS SEQRES 11 A 165 LEU ILE LEU ILE ALA SER ARG ASP ILE ALA ALA GLY GLU SEQRES 12 A 165 GLU LEU LEU TYR ASP TYR GLY ASP ARG SER LYS ALA SER SEQRES 13 A 165 ILE GLU ALA HIS PRO TRP LEU LYS HIS SEQRES 1 B 165 ALA MET GLY SER ARG LYS SER LYS ALA GLU LEU GLN SER SEQRES 2 B 165 GLU GLU ARG LYS ARG ILE ASP GLU LEU ILE GLU SER GLY SEQRES 3 B 165 LYS GLU GLU GLY MET LYS ILE ASP LEU ILE ASP GLY LYS SEQRES 4 B 165 GLY ARG GLY VAL ILE ALA THR LYS GLN PHE SER ARG GLY SEQRES 5 B 165 ASP PHE VAL VAL GLU TYR HIS GLY ASP LEU ILE GLU ILE SEQRES 6 B 165 THR ASP ALA LYS LYS ARG GLU ALA LEU TYR ALA GLN ASP SEQRES 7 B 165 PRO SER THR GLY CYS TYR MET TYR TYR PHE GLN TYR LEU SEQRES 8 B 165 SER LYS THR TYR CYS VAL ASP ALA THR ARG GLU THR ASN SEQRES 9 B 165 ARG LEU GLY ARG LEU ILE ASN HIS SER LYS SER GLY ASN SEQRES 10 B 165 CYS GLN THR LYS LEU HIS ASP ILE ASP GLY VAL PRO HIS SEQRES 11 B 165 LEU ILE LEU ILE ALA SER ARG ASP ILE ALA ALA GLY GLU SEQRES 12 B 165 GLU LEU LEU TYR ASP TYR GLY ASP ARG SER LYS ALA SER SEQRES 13 B 165 ILE GLU ALA HIS PRO TRP LEU LYS HIS SEQRES 1 I 10 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK HET SAM A 501 27 HET UNX A 502 1 HET UNX A 503 1 HET UNX A 504 1 HET UNX A 505 1 HET UNX A 506 1 HET UNX A 507 1 HET UNX A 508 1 HET UNX A 509 1 HET UNX A 510 1 HET UNX A 511 1 HET UNX A 512 1 HET UNX A 513 1 HET UNX A 514 1 HET SAM B 501 27 HET UNX B 502 1 HET UNX B 503 1 HET UNX B 504 1 HET UNX B 505 1 HET UNX B 506 1 HET UNX B 507 1 HET UNX B 508 1 HET UNX B 509 1 HET UNX B 510 1 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 4 SAM 2(C15 H22 N6 O5 S) FORMUL 5 UNX 22(X) FORMUL 28 HOH *130(H2 O) HELIX 1 1 SER A 235 GLY A 254 1 20 HELIX 2 2 ASP A 295 GLN A 305 1 11 HELIX 3 3 GLN A 305 GLY A 310 1 6 HELIX 4 4 LEU A 334 ILE A 338 5 5 HELIX 5 5 SER A 381 HIS A 388 1 8 HELIX 6 6 PRO A 389 HIS A 393 5 5 HELIX 7 7 LYS B 245 GLY B 254 1 10 HELIX 8 8 ASP B 295 GLN B 305 1 11 HELIX 9 9 GLN B 305 GLY B 310 1 6 HELIX 10 10 LEU B 334 ILE B 338 5 5 HELIX 11 11 SER B 381 HIS B 388 1 8 HELIX 12 12 PRO B 389 HIS B 393 5 5 HELIX 13 13 UNK I 5 UNK I 12 1 8 SHEET 1 A 2 MET A 259 ILE A 264 0 SHEET 2 A 2 GLY A 268 ALA A 273 -1 O GLY A 268 N ILE A 264 SHEET 1 B 3 PHE A 282 GLU A 285 0 SHEET 2 B 3 VAL A 356 ALA A 363 -1 O LEU A 361 N VAL A 283 SHEET 3 B 3 CYS A 346 ILE A 353 -1 N LYS A 349 O ILE A 360 SHEET 1 C 3 ASP A 289 ILE A 293 0 SHEET 2 C 3 LYS A 321 ASP A 326 -1 O ASP A 326 N ASP A 289 SHEET 3 C 3 MET A 313 TYR A 318 -1 N PHE A 316 O TYR A 323 SHEET 1 D 2 ASN A 339 HIS A 340 0 SHEET 2 D 2 LEU A 374 TYR A 375 1 O TYR A 375 N ASN A 339 SHEET 1 E 2 MET B 259 ILE B 264 0 SHEET 2 E 2 GLY B 268 ALA B 273 -1 O GLY B 268 N ILE B 264 SHEET 1 F 3 PHE B 282 GLU B 285 0 SHEET 2 F 3 VAL B 356 ALA B 363 -1 O LEU B 361 N VAL B 284 SHEET 3 F 3 CYS B 346 ILE B 353 -1 N HIS B 351 O HIS B 358 SHEET 1 G 3 ASP B 289 ILE B 293 0 SHEET 2 G 3 LYS B 321 ASP B 326 -1 O CYS B 324 N ILE B 291 SHEET 3 G 3 MET B 313 TYR B 318 -1 N PHE B 316 O TYR B 323 SHEET 1 H 2 ASN B 339 HIS B 340 0 SHEET 2 H 2 LEU B 374 TYR B 375 1 O TYR B 375 N ASN B 339 SITE 1 AC1 17 GLY A 266 LYS A 267 ARG A 269 CYS A 311 SITE 2 AC1 17 TYR A 312 ARG A 336 LEU A 337 ILE A 338 SITE 3 AC1 17 ASN A 339 HIS A 340 TYR A 377 TRP A 390 SITE 4 AC1 17 HOH A 609 HOH A 613 HOH A 615 HOH A 618 SITE 5 AC1 17 ALA B 387 SITE 1 AC2 17 ALA A 387 HOH A 601 HOH A 613 GLY B 266 SITE 2 AC2 17 LYS B 267 ARG B 269 CYS B 311 TYR B 312 SITE 3 AC2 17 ARG B 336 LEU B 337 ILE B 338 ASN B 339 SITE 4 AC2 17 HIS B 340 TYR B 377 TRP B 390 HOH B 611 SITE 5 AC2 17 HOH B 621 CRYST1 101.439 101.439 140.799 90.00 90.00 120.00 P 61 2 2 24 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 0.009858 0.005692 0.000000 0.00000 SCALE2 0.000000 0.011383 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007102 0.00000