HEADER PROTEIN BINDING 16-MAR-21 7EDP TITLE CRYSTAL STRUCTURE OF AF10-DOT1L COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: DOT1-LIKE PROTEIN,HISTONE H3-K79 METHYLTRANSFERASE,H3-K79- COMPND 5 HMTASE,LYSINE N-METHYLTRANSFERASE 4; COMPND 6 EC: 2.1.1.360; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROTEIN AF-10; COMPND 10 CHAIN: A; COMPND 11 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: DOT1L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: MLLT10; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.CHEN,Z.ZHOU REVDAT 4 29-NOV-23 7EDP 1 REMARK REVDAT 3 16-FEB-22 7EDP 1 JRNL REVDAT 2 10-NOV-21 7EDP 1 JRNL REVDAT 1 28-APR-21 7EDP 0 JRNL AUTH Z.ZHOU,S.KANG,Z.HUANG,Z.ZHOU,S.CHEN JRNL TITL STRUCTURAL CHARACTERISTICS OF COILED-COIL REGIONS IN JRNL TITL 2 AF10-DOT1L AND AF10-INHIBITORY PEPTIDE COMPLEX. JRNL REF J LEUKOC BIOL V. 110 1091 2021 JRNL REFN ISSN 1938-3673 JRNL PMID 33993518 JRNL DOI 10.1002/JLB.1MA0421-010R REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1951 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 6763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.290 REMARK 3 FREE R VALUE TEST SET COUNT : 696 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 31.8260 - 3.7598 0.99 1356 158 0.1891 0.2287 REMARK 3 2 3.7598 - 2.9850 1.00 1283 147 0.2235 0.2897 REMARK 3 3 2.9850 - 2.6079 1.00 1243 143 0.2508 0.3072 REMARK 3 4 2.6079 - 2.3695 0.99 1225 144 0.2722 0.2851 REMARK 3 5 2.3695 - 2.2000 0.78 960 104 0.3068 0.3957 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.00 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 : 0.007 653 REMARK 3 ANGLE : 0.866 873 REMARK 3 CHIRALITY : 0.033 110 REMARK 3 PLANARITY : 0.003 110 REMARK 3 DIHEDRAL : 17.726 259 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 610 THROUGH 649 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2570 9.3514 63.0941 REMARK 3 T TENSOR REMARK 3 T11: 0.3846 T22: 0.3283 REMARK 3 T33: 0.2847 T12: 0.0205 REMARK 3 T13: 0.0164 T23: 0.0698 REMARK 3 L TENSOR REMARK 3 L11: 2.5096 L22: 8.5304 REMARK 3 L33: 4.5210 L12: 0.4323 REMARK 3 L13: 1.3694 L23: 6.0441 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: -0.2642 S13: 0.1659 REMARK 3 S21: 0.4335 S22: -0.4327 S23: 0.1770 REMARK 3 S31: -0.2062 S32: -0.9372 S33: 0.3523 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 754 THROUGH 796 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2974 12.3574 54.1010 REMARK 3 T TENSOR REMARK 3 T11: 0.7157 T22: 0.4398 REMARK 3 T33: 0.3160 T12: -0.0412 REMARK 3 T13: -0.0172 T23: 0.0591 REMARK 3 L TENSOR REMARK 3 L11: 2.5483 L22: 1.0678 REMARK 3 L33: 8.0643 L12: 0.9627 REMARK 3 L13: 3.6000 L23: 2.5035 REMARK 3 S TENSOR REMARK 3 S11: 0.0573 S12: 0.0502 S13: 0.0947 REMARK 3 S21: 0.0074 S22: -0.1221 S23: -0.0715 REMARK 3 S31: -1.0358 S32: 0.3539 S33: 0.1089 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 7EDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6826 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 31.826 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 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: PHENIX REMARK 200 STARTING MODEL: 1ZIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 52.48167 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 104.96333 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 104.96333 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 52.48167 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 ASP B 610 CG OD1 OD2 REMARK 470 TRP B 611 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 611 CZ3 CH2 REMARK 470 LYS B 618 CG CD CE NZ REMARK 470 LYS B 621 CD CE NZ REMARK 470 LYS B 649 CD CE NZ REMARK 470 LYS A 778 CD CE 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 HOH A 809 O HOH A 815 1.93 REMARK 500 O HOH A 813 O HOH A 816 2.02 REMARK 500 O HOH B 705 O HOH A 803 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EDP B 610 649 UNP Q8TEK3 DOT1L_HUMAN 610 649 DBREF 7EDP A 754 796 UNP Q5JT35 Q5JT35_HUMAN 433 475 SEQRES 1 B 40 ASP TRP ALA THR LEU SER LEU GLU LYS LEU LEU LYS GLU SEQRES 2 B 40 LYS GLN ALA LEU LYS SER GLN ILE SER GLU LYS GLN ARG SEQRES 3 B 40 HIS CYS LEU GLU LEU GLN ILE SER ILE VAL GLU LEU GLU SEQRES 4 B 40 LYS SEQRES 1 A 43 SER ASP ILE LEU GLY MET LEU LYS SER LEU HIS GLN LEU SEQRES 2 A 43 GLN VAL GLU ASN ARG ARG LEU GLU GLU GLN ILE LYS ASN SEQRES 3 A 43 LEU THR ALA LYS LYS GLU ARG LEU GLN LEU LEU ASN ALA SEQRES 4 A 43 GLN LEU SER VAL FORMUL 3 HOH *34(H2 O) HELIX 1 AA1 ASP B 610 LYS B 649 1 40 HELIX 2 AA2 ASP A 755 LEU A 794 1 40 CRYST1 37.524 37.524 157.445 90.00 90.00 120.00 P 31 2 1 6 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 0.026650 0.015386 0.000000 0.00000 SCALE2 0.000000 0.030772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006351 0.00000