PDB Short entry for 4YNM HEADER TRANSFERASE 10-MAR-15 4YNM TITLE ASH1L WILD-TYPE SET DOMAIN IN COMPLEX WITH S-ADENOSYL METHIONINE (SAM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE ASH1L; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SET DOMAIN (UNP RESIDUES 2074-2293); COMPND 5 SYNONYM: ASH1-LIKE PROTEIN,HUASH1,ABSENT SMALL AND HOMEOTIC DISKS COMPND 6 PROTEIN 1 HOMOLOG,LYSINE N-METHYLTRANSFERASE 2H; COMPND 7 EC: 2.1.1.43; COMPND 8 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: ASH1L, KIAA1420, KMT2H; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE METHYLATION, SET DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.S.ROGAWSKI,J.NDOJ,H.-J.CHO,I.MAILLARD,J.GREMBECKA,T.CIERPICKI REVDAT 7 27-SEP-23 4YNM 1 REMARK REVDAT 6 04-DEC-19 4YNM 1 REMARK REVDAT 5 04-OCT-17 4YNM 1 REMARK REVDAT 4 27-SEP-17 4YNM 1 JRNL REMARK REVDAT 3 16-SEP-15 4YNM 1 JRNL REVDAT 2 09-SEP-15 4YNM 1 JRNL REVDAT 1 02-SEP-15 4YNM 0 JRNL AUTH D.S.ROGAWSKI,J.NDOJ,H.J.CHO,I.MAILLARD,J.GREMBECKA, JRNL AUTH 2 T.CIERPICKI JRNL TITL TWO LOOPS UNDERGOING CONCERTED DYNAMICS REGULATE THE JRNL TITL 2 ACTIVITY OF THE ASH1L HISTONE METHYLTRANSFERASE. JRNL REF BIOCHEMISTRY V. 54 5401 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26292256 JRNL DOI 10.1021/ACS.BIOCHEM.5B00697 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23762 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) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1271 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1664 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3333 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.04000 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): 0.323 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.238 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.875 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3464 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4664 ; 1.769 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 408 ; 6.998 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;38.596 ;24.086 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 608 ;18.653 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;25.239 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 470 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2681 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2045 ; 1.099 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3285 ; 2.071 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1419 ; 2.993 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1379 ; 4.678 ; 4.500 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2069 A 2256 3 REMARK 3 1 B 2069 B 2256 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 684 ; 0.110 ; 0.050 REMARK 3 LOOSE POSITIONAL 1 A (A): 716 ; 0.270 ; 5.000 REMARK 3 TIGHT THERMAL 1 A (A**2): 684 ; 0.350 ; 0.500 REMARK 3 LOOSE THERMAL 1 A (A**2): 716 ; 0.400 ;10.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2266 A 2280 3 REMARK 3 1 B 2266 B 2280 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 A (A): 56 ; 0.100 ; 0.050 REMARK 3 LOOSE POSITIONAL 2 A (A): 52 ; 0.110 ; 5.000 REMARK 3 TIGHT THERMAL 2 A (A**2): 56 ; 0.310 ; 0.500 REMARK 3 LOOSE THERMAL 2 A (A**2): 52 ; 0.260 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4YNM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000206377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 7.3-7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25099 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3OPE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, 20 MM TRIS, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 153.98867 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 76.99433 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 76.99433 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 153.98867 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 2063 REMARK 465 ALA A 2064 REMARK 465 MET A 2065 REMARK 465 GLY A 2281 REMARK 465 LYS A 2282 REMARK 465 SER A 2283 REMARK 465 GLN A 2284 REMARK 465 ARG A 2285 REMARK 465 VAL A 2286 REMARK 465 ASN A 2287 REMARK 465 GLY A 2288 REMARK 465 GLY B 2063 REMARK 465 ALA B 2064 REMARK 465 MET B 2065 REMARK 465 ALA B 2066 REMARK 465 GLU B 2087 REMARK 465 ALA B 2088 REMARK 465 THR B 2089 REMARK 465 THR B 2090 REMARK 465 CYS B 2091 REMARK 465 ASN B 2092 REMARK 465 CYS B 2093 REMARK 465 LYS B 2094 REMARK 465 LYS B 2095 REMARK 465 PRO B 2096 REMARK 465 ASP B 2097 REMARK 465 ASP B 2098 REMARK 465 ASP B 2099 REMARK 465 THR B 2100 REMARK 465 ARG B 2101 REMARK 465 LYS B 2102 REMARK 465 GLY B 2103 REMARK 465 GLY B 2280 REMARK 465 GLY B 2281 REMARK 465 LYS B 2282 REMARK 465 SER B 2283 REMARK 465 GLN B 2284 REMARK 465 ARG B 2285 REMARK 465 VAL B 2286 REMARK 465 ASN B 2287 REMARK 465 GLY B 2288 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 OD2 ASP B 2199 NZ LYS B 2228 1.97 REMARK 500 OD1 ASP A 2199 NZ LYS A 2228 2.19 REMARK 500 OG1 THR A 2121 O HOH A 2401 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 CE LYS A 2081 CG1 ILE B 2184 4455 1.93 REMARK 500 NH1 ARG A 2208 CD2 PHE B 2257 1545 2.17 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 A2144 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A2199 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A2199 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A2236 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 TYR B2086 CA - CB - CG ANGL. DEV. = 12.4 DEGREES REMARK 500 TYR B2086 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 TYR B2086 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B2132 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B2132 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 MET B2245 CG - SD - CE ANGL. DEV. = -9.7 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 A2078 -84.19 -91.41 REMARK 500 THR A2090 81.98 43.64 REMARK 500 CYS A2104 65.70 39.52 REMARK 500 VAL A2105 -94.12 -110.41 REMARK 500 ASP A2106 40.37 -95.40 REMARK 500 ASP A2107 16.94 168.11 REMARK 500 GLN A2131 31.43 -141.21 REMARK 500 GLU A2149 -4.90 80.29 REMARK 500 LEU A2198 -64.85 -109.61 REMARK 500 ASP A2199 168.92 173.38 REMARK 500 SER A2200 50.44 33.37 REMARK 500 GLU A2263 6.35 87.81 REMARK 500 VAL B2078 -80.33 -93.27 REMARK 500 VAL B2105 -96.87 -117.37 REMARK 500 ASP B2106 42.22 -94.39 REMARK 500 ASP B2107 19.16 165.69 REMARK 500 GLU B2149 -9.31 84.49 REMARK 500 LEU B2198 -147.60 -92.24 REMARK 500 ASP B2199 -161.18 -120.52 REMARK 500 GLU B2263 34.14 -98.33 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 A2303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A2091 SG REMARK 620 2 CYS A2093 SG 110.0 REMARK 620 3 CYS A2104 SG 104.1 106.9 REMARK 620 4 CYS A2108 SG 121.2 104.7 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A2104 SG REMARK 620 2 CYS A2117 SG 110.3 REMARK 620 3 CYS A2122 SG 100.1 118.1 REMARK 620 4 CYS A2128 SG 117.2 111.9 98.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A2220 SG REMARK 620 2 CYS A2268 SG 107.8 REMARK 620 3 CYS A2270 SG 110.4 109.9 REMARK 620 4 CYS A2275 SG 108.4 106.1 114.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B2104 SG REMARK 620 2 CYS B2117 SG 92.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B2104 SG REMARK 620 2 CYS B2108 SG 84.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B2220 SG REMARK 620 2 CYS B2268 SG 114.7 REMARK 620 3 CYS B2270 SG 110.0 107.9 REMARK 620 4 CYS B2275 SG 109.5 101.7 112.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 2301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 2302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 2303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 2304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 2301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 2302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 2303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM B 2304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YNP RELATED DB: PDB DBREF 4YNM A 2069 2288 UNP Q9NR48 ASH1L_HUMAN 2074 2293 DBREF 4YNM B 2069 2288 UNP Q9NR48 ASH1L_HUMAN 2074 2293 SEQADV 4YNM GLY A 2063 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM ALA A 2064 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM MET A 2065 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM ALA A 2066 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM GLY A 2067 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM SER A 2068 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM GLY B 2063 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM ALA B 2064 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM MET B 2065 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM ALA B 2066 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM GLY B 2067 UNP Q9NR48 EXPRESSION TAG SEQADV 4YNM SER B 2068 UNP Q9NR48 EXPRESSION TAG SEQRES 1 A 226 GLY ALA MET ALA GLY SER TYR LYS LYS ILE ARG SER ASN SEQRES 2 A 226 VAL TYR VAL ASP VAL LYS PRO LEU SER GLY TYR GLU ALA SEQRES 3 A 226 THR THR CYS ASN CYS LYS LYS PRO ASP ASP ASP THR ARG SEQRES 4 A 226 LYS GLY CYS VAL ASP ASP CYS LEU ASN ARG MET ILE PHE SEQRES 5 A 226 ALA GLU CYS SER PRO ASN THR CYS PRO CYS GLY GLU GLN SEQRES 6 A 226 CYS CYS ASN GLN ARG ILE GLN ARG HIS GLU TRP VAL GLN SEQRES 7 A 226 CYS LEU GLU ARG PHE ARG ALA GLU GLU LYS GLY TRP GLY SEQRES 8 A 226 ILE ARG THR LYS GLU PRO LEU LYS ALA GLY GLN PHE ILE SEQRES 9 A 226 ILE GLU TYR LEU GLY GLU VAL VAL SER GLU GLN GLU PHE SEQRES 10 A 226 ARG ASN ARG MET ILE GLU GLN TYR HIS ASN HIS SER ASP SEQRES 11 A 226 HIS TYR CYS LEU ASN LEU ASP SER GLY MET VAL ILE ASP SEQRES 12 A 226 SER TYR ARG MET GLY ASN GLU ALA ARG PHE ILE ASN HIS SEQRES 13 A 226 SER CYS ASP PRO ASN CYS GLU MET GLN LYS TRP SER VAL SEQRES 14 A 226 ASN GLY VAL TYR ARG ILE GLY LEU TYR ALA LEU LYS ASP SEQRES 15 A 226 MET PRO ALA GLY THR GLU LEU THR TYR ASP TYR ASN PHE SEQRES 16 A 226 HIS SER PHE ASN VAL GLU LYS GLN GLN LEU CYS LYS CYS SEQRES 17 A 226 GLY PHE GLU LYS CYS ARG GLY ILE ILE GLY GLY LYS SER SEQRES 18 A 226 GLN ARG VAL ASN GLY SEQRES 1 B 226 GLY ALA MET ALA GLY SER TYR LYS LYS ILE ARG SER ASN SEQRES 2 B 226 VAL TYR VAL ASP VAL LYS PRO LEU SER GLY TYR GLU ALA SEQRES 3 B 226 THR THR CYS ASN CYS LYS LYS PRO ASP ASP ASP THR ARG SEQRES 4 B 226 LYS GLY CYS VAL ASP ASP CYS LEU ASN ARG MET ILE PHE SEQRES 5 B 226 ALA GLU CYS SER PRO ASN THR CYS PRO CYS GLY GLU GLN SEQRES 6 B 226 CYS CYS ASN GLN ARG ILE GLN ARG HIS GLU TRP VAL GLN SEQRES 7 B 226 CYS LEU GLU ARG PHE ARG ALA GLU GLU LYS GLY TRP GLY SEQRES 8 B 226 ILE ARG THR LYS GLU PRO LEU LYS ALA GLY GLN PHE ILE SEQRES 9 B 226 ILE GLU TYR LEU GLY GLU VAL VAL SER GLU GLN GLU PHE SEQRES 10 B 226 ARG ASN ARG MET ILE GLU GLN TYR HIS ASN HIS SER ASP SEQRES 11 B 226 HIS TYR CYS LEU ASN LEU ASP SER GLY MET VAL ILE ASP SEQRES 12 B 226 SER TYR ARG MET GLY ASN GLU ALA ARG PHE ILE ASN HIS SEQRES 13 B 226 SER CYS ASP PRO ASN CYS GLU MET GLN LYS TRP SER VAL SEQRES 14 B 226 ASN GLY VAL TYR ARG ILE GLY LEU TYR ALA LEU LYS ASP SEQRES 15 B 226 MET PRO ALA GLY THR GLU LEU THR TYR ASP TYR ASN PHE SEQRES 16 B 226 HIS SER PHE ASN VAL GLU LYS GLN GLN LEU CYS LYS CYS SEQRES 17 B 226 GLY PHE GLU LYS CYS ARG GLY ILE ILE GLY GLY LYS SER SEQRES 18 B 226 GLN ARG VAL ASN GLY HET ZN A2301 1 HET ZN A2302 1 HET ZN A2303 1 HET SAM A2304 27 HET ZN B2301 1 HET ZN B2302 1 HET ZN B2303 1 HET SAM B2304 27 HETNAM ZN ZINC ION HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 3 ZN 6(ZN 2+) FORMUL 6 SAM 2(C15 H22 N6 O5 S) FORMUL 11 HOH *104(H2 O) HELIX 1 AA1 CYS A 2108 ILE A 2113 1 6 HELIX 2 AA2 CYS A 2124 CYS A 2128 5 5 HELIX 3 AA3 GLU A 2176 GLN A 2186 1 11 HELIX 4 AA4 ASN A 2211 ILE A 2216 5 6 HELIX 5 AA5 ASP A 2254 SER A 2259 1 6 HELIX 6 AA6 ASN B 2110 PHE B 2114 5 5 HELIX 7 AA7 CYS B 2124 CYS B 2128 5 5 HELIX 8 AA8 GLU B 2176 GLN B 2186 1 11 HELIX 9 AA9 ASN B 2211 ILE B 2216 5 6 HELIX 10 AB1 ASP B 2254 SER B 2259 1 6 SHEET 1 AA1 2 LYS A2070 LYS A2071 0 SHEET 2 AA1 2 MET A2209 GLY A2210 1 O GLY A2210 N LYS A2070 SHEET 1 AA2 4 VAL A2076 TYR A2077 0 SHEET 2 AA2 4 GLU A2172 SER A2175 1 O VAL A2173 N VAL A2076 SHEET 3 AA2 4 MET A2202 ASP A2205 -1 O ASP A2205 N GLU A2172 SHEET 4 AA2 4 CYS A2195 ASP A2199 -1 N LEU A2196 O ILE A2204 SHEET 1 AA3 2 LEU A2142 ARG A2146 0 SHEET 2 AA3 2 TRP A2152 THR A2156 -1 O GLY A2153 N PHE A2145 SHEET 1 AA4 3 PHE A2165 GLU A2168 0 SHEET 2 AA4 3 VAL A2234 ALA A2241 -1 O LEU A2239 N ILE A2167 SHEET 3 AA4 3 CYS A2224 VAL A2231 -1 N TRP A2229 O ARG A2236 SHEET 1 AA5 2 ASN A2217 HIS A2218 0 SHEET 2 AA5 2 THR A2252 TYR A2253 1 O TYR A2253 N ASN A2217 SHEET 1 AA6 2 GLN A2266 LEU A2267 0 SHEET 2 AA6 2 ILE A2278 ILE A2279 -1 O ILE A2279 N GLN A2266 SHEET 1 AA7 2 LYS B2070 LYS B2071 0 SHEET 2 AA7 2 MET B2209 GLY B2210 1 O GLY B2210 N LYS B2070 SHEET 1 AA8 4 VAL B2076 TYR B2077 0 SHEET 2 AA8 4 GLU B2172 SER B2175 1 O VAL B2173 N VAL B2076 SHEET 3 AA8 4 MET B2202 ASP B2205 -1 O ASP B2205 N GLU B2172 SHEET 4 AA8 4 CYS B2195 ASN B2197 -1 N LEU B2196 O ILE B2204 SHEET 1 AA9 2 LEU B2142 ARG B2146 0 SHEET 2 AA9 2 TRP B2152 THR B2156 -1 O GLY B2153 N PHE B2145 SHEET 1 AB1 3 PHE B2165 GLU B2168 0 SHEET 2 AB1 3 VAL B2234 ALA B2241 -1 O LEU B2239 N ILE B2166 SHEET 3 AB1 3 CYS B2224 VAL B2231 -1 N VAL B2231 O VAL B2234 SHEET 1 AB2 2 ASN B2217 HIS B2218 0 SHEET 2 AB2 2 THR B2252 TYR B2253 1 O TYR B2253 N ASN B2217 SSBOND 1 CYS B 2122 CYS B 2128 1555 1555 2.06 LINK SG CYS A2091 ZN ZN A2303 1555 1555 1.96 LINK SG CYS A2093 ZN ZN A2303 1555 1555 2.35 LINK SG CYS A2104 ZN ZN A2302 1555 1555 2.26 LINK SG CYS A2104 ZN ZN A2303 1555 1555 2.18 LINK SG CYS A2108 ZN ZN A2303 1555 1555 2.35 LINK SG CYS A2117 ZN ZN A2302 1555 1555 2.11 LINK SG CYS A2122 ZN ZN A2302 1555 1555 2.25 LINK SG CYS A2128 ZN ZN A2302 1555 1555 2.05 LINK SG CYS A2220 ZN ZN A2301 1555 1555 2.35 LINK SG CYS A2268 ZN ZN A2301 1555 1555 2.24 LINK SG CYS A2270 ZN ZN A2301 1555 1555 2.23 LINK SG CYS A2275 ZN ZN A2301 1555 1555 2.31 LINK SG CYS B2104 ZN ZN B2302 1555 1555 2.21 LINK SG CYS B2104 ZN ZN B2303 1555 1555 1.99 LINK SG CYS B2108 ZN ZN B2303 1555 1555 2.67 LINK SG CYS B2117 ZN ZN B2302 1555 1555 2.47 LINK SG CYS B2220 ZN ZN B2301 1555 1555 2.23 LINK SG CYS B2268 ZN ZN B2301 1555 1555 2.21 LINK SG CYS B2270 ZN ZN B2301 1555 1555 2.05 LINK SG CYS B2275 ZN ZN B2301 1555 1555 2.46 SITE 1 AC1 4 CYS A2220 CYS A2268 CYS A2270 CYS A2275 SITE 1 AC2 4 CYS A2104 CYS A2117 CYS A2122 CYS A2128 SITE 1 AC3 4 CYS A2091 CYS A2093 CYS A2104 CYS A2108 SITE 1 AC4 19 LYS A2150 GLY A2151 TRP A2152 SER A2191 SITE 2 AC4 19 ASP A2192 HIS A2193 TYR A2194 ARG A2214 SITE 3 AC4 19 PHE A2215 ASN A2217 HIS A2218 TYR A2255 SITE 4 AC4 19 GLN A2266 LEU A2267 CYS A2268 LYS A2269 SITE 5 AC4 19 ILE A2279 HOH A2418 HOH A2422 SITE 1 AC5 4 CYS B2220 CYS B2268 CYS B2270 CYS B2275 SITE 1 AC6 5 CYS B2104 CYS B2117 CYS B2122 CYS B2128 SITE 2 AC6 5 ZN B2303 SITE 1 AC7 4 CYS B2104 CYS B2108 CYS B2117 ZN B2302 SITE 1 AC8 17 LYS B2150 TRP B2152 SER B2191 ASP B2192 SITE 2 AC8 17 HIS B2193 TYR B2194 ARG B2214 PHE B2215 SITE 3 AC8 17 ASN B2217 HIS B2218 TYR B2255 GLN B2266 SITE 4 AC8 17 LEU B2267 CYS B2268 LYS B2269 ILE B2279 SITE 5 AC8 17 HOH B2413 CRYST1 59.141 59.141 230.983 90.00 90.00 120.00 P 32 2 1 12 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 0.016909 0.009762 0.000000 0.00000 SCALE2 0.000000 0.019525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004329 0.00000