HEADER TRANSCRIPTION 25-FEB-21 7E7C TITLE CRYSTAL STRUCTURE OF ENL YEATS DOMAIN T1 MUTANT IN COMPLEX WITH TITLE 2 HISTONE H3 ACETYLATION AT K27 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ENL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YEATS DOMAIN-CONTAINING PROTEIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H3K27AC(24-27) PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 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: MLLT1, ENL, LTG19, YEATS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS YEATS DOMAIN, COMPLEX, HISTONE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,H.LI REVDAT 2 29-NOV-23 7E7C 1 REMARK REVDAT 1 06-APR-22 7E7C 0 JRNL AUTH Y.LI,H.LI JRNL TITL CRYSTAL STRUCTURE OF ENL YEATS DOMAIN T1 MUTANT IN COMPLEX JRNL TITL 2 WITH HISTONE H3 ACETYLATION AT K27 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 14106 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1411 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 34.3500 - 3.9600 0.98 1381 153 0.2143 0.1987 REMARK 3 2 3.9500 - 3.1400 1.00 1308 145 0.1883 0.2566 REMARK 3 3 3.1400 - 2.7400 0.98 1275 143 0.2309 0.2897 REMARK 3 4 2.7400 - 2.4900 1.00 1291 142 0.2427 0.2785 REMARK 3 5 2.4900 - 2.3100 0.99 1274 142 0.2239 0.3012 REMARK 3 6 2.3100 - 2.1800 0.99 1268 141 0.2230 0.2777 REMARK 3 7 2.1800 - 2.0700 0.98 1238 138 0.2114 0.2734 REMARK 3 8 2.0700 - 1.9800 0.99 1264 141 0.2176 0.2515 REMARK 3 9 1.9800 - 1.9000 0.98 1230 136 0.2201 0.2769 REMARK 3 10 1.9000 - 1.8400 0.93 1166 130 0.2540 0.3092 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.69 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7E7C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9779 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14147 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 0.81600 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: MOLREP REMARK 200 STARTING MODEL: 5J9S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 0.1M MES PH 6.5, 0.2M REMARK 280 POTASSIUM IODIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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 -X+1/2,Y+1/2,-Z 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 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 -1.000000 0.000000 0.000000 19.31750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.03250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.31750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.03250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 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 350 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLU A 149 REMARK 465 GLY A 150 REMARK 465 ALA A 151 REMARK 465 HIS A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 60 N PRO A 60 CA 0.228 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 PRO A 60 C - N - CA ANGL. DEV. = 18.7 DEGREES REMARK 500 PRO A 60 CA - N - CD ANGL. DEV. = -10.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7E7C A 1 151 UNP Q03111 ENL_HUMAN 1 148 DBREF 7E7C B 24 27 PDB 7E7C 7E7C 24 27 SEQADV 7E7C GLY A -2 UNP Q03111 EXPRESSION TAG SEQADV 7E7C SER A -1 UNP Q03111 EXPRESSION TAG SEQADV 7E7C HIS A 0 UNP Q03111 EXPRESSION TAG SEQADV 7E7C ASN A 115 UNP Q03111 INSERTION SEQADV 7E7C HIS A 116 UNP Q03111 INSERTION SEQADV 7E7C LEU A 117 UNP Q03111 INSERTION SEQADV 7E7C HIS A 152 UNP Q03111 EXPRESSION TAG SEQADV 7E7C HIS A 153 UNP Q03111 EXPRESSION TAG SEQADV 7E7C HIS A 154 UNP Q03111 EXPRESSION TAG SEQADV 7E7C HIS A 155 UNP Q03111 EXPRESSION TAG SEQADV 7E7C HIS A 156 UNP Q03111 EXPRESSION TAG SEQADV 7E7C HIS A 157 UNP Q03111 EXPRESSION TAG SEQRES 1 A 160 GLY SER HIS MET ASP ASN GLN CYS THR VAL GLN VAL ARG SEQRES 2 A 160 LEU GLU LEU GLY HIS ARG ALA GLN LEU ARG LYS LYS PRO SEQRES 3 A 160 THR THR GLU GLY PHE THR HIS ASP TRP MET VAL PHE VAL SEQRES 4 A 160 ARG GLY PRO GLU GLN CYS ASP ILE GLN HIS PHE VAL GLU SEQRES 5 A 160 LYS VAL VAL PHE TRP LEU HIS ASP SER PHE PRO LYS PRO SEQRES 6 A 160 ARG ARG VAL CYS LYS GLU PRO PRO TYR LYS VAL GLU GLU SEQRES 7 A 160 SER GLY TYR ALA GLY PHE ILE MET PRO ILE GLU VAL HIS SEQRES 8 A 160 PHE LYS ASN LYS GLU GLU PRO ARG LYS VAL CYS PHE THR SEQRES 9 A 160 TYR ASP LEU PHE LEU ASN LEU GLU GLY ASN PRO PRO VAL SEQRES 10 A 160 ASN HIS LEU ASN HIS LEU ARG CYS GLU LYS LEU THR PHE SEQRES 11 A 160 ASN ASN PRO THR THR GLU PHE ARG TYR LYS LEU LEU ARG SEQRES 12 A 160 ALA GLY GLY VAL MET VAL MET PRO GLU GLY ALA HIS HIS SEQRES 13 A 160 HIS HIS HIS HIS SEQRES 1 B 4 ALA ALA ARG ALY HET ALY B 27 12 HET EDO A 201 4 HET EDO A 202 4 HET IOD A 203 1 HET IOD A 204 1 HETNAM ALY N(6)-ACETYLLYSINE HETNAM EDO 1,2-ETHANEDIOL HETNAM IOD IODIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ALY C8 H16 N2 O3 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 IOD 2(I 1-) FORMUL 7 HOH *53(H2 O) HELIX 1 AA1 ASP A 43 HIS A 46 5 4 HELIX 2 AA2 THR A 131 ALA A 141 1 11 SHEET 1 AA1 4 TYR A 71 GLY A 77 0 SHEET 2 AA1 4 HIS A 30 ARG A 37 -1 N TRP A 32 O GLU A 75 SHEET 3 AA1 4 THR A 6 LEU A 19 -1 N GLY A 14 O PHE A 35 SHEET 4 AA1 4 HIS A 116 ASN A 128 -1 O LEU A 125 N VAL A 9 SHEET 1 AA2 4 TYR A 71 GLY A 77 0 SHEET 2 AA2 4 HIS A 30 ARG A 37 -1 N TRP A 32 O GLU A 75 SHEET 3 AA2 4 THR A 6 LEU A 19 -1 N GLY A 14 O PHE A 35 SHEET 4 AA2 4 VAL A 144 MET A 145 -1 O VAL A 144 N GLN A 8 SHEET 1 AA3 4 ARG A 63 CYS A 66 0 SHEET 2 AA3 4 VAL A 48 TRP A 54 -1 N PHE A 53 O ARG A 64 SHEET 3 AA3 4 PHE A 81 PHE A 89 -1 O PRO A 84 N TRP A 54 SHEET 4 AA3 4 LYS A 97 LEU A 104 -1 O TYR A 102 N MET A 83 LINK C ARG B 26 N ALY B 27 1555 1555 1.32 CISPEP 1 PRO A 69 PRO A 70 0 2.97 CISPEP 2 GLU A 94 PRO A 95 0 -5.07 CRYST1 38.635 118.065 34.350 90.00 90.00 90.00 P 21 21 2 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 0.025883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029112 0.00000