HEADER PEPTIDE BINDING PROTEIN 22-SEP-22 8B5A TITLE HUMAN BRD3 BROMODOMAIN 2 IN COMPLEX WITH A H4 PEPTIDE CONTAINING TITLE 2 APMTRI (H4K20APMTRI) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RING3-LIKE PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: H4K20APMTRI; 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: BRD3, KIAA0043, RING3L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS APMTRI, ACETYL-LYSINE MIMIC, BET-BROMODOMAIN, HISTONE-PEPTIDE, KEYWDS 2 PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.B.BRAUN,N.BARTLICK,T.STEHLE REVDAT 6 07-FEB-24 8B5A 1 LINK REVDAT 5 24-MAY-23 8B5A 1 FORMUL REVDAT 4 22-MAR-23 8B5A 1 JRNL REVDAT 3 15-MAR-23 8B5A 1 JRNL REVDAT 2 15-FEB-23 8B5A 1 JRNL REVDAT 1 11-JAN-23 8B5A 0 JRNL AUTH S.KIRCHGASSNER,M.B.BRAUN,N.BARTLICK,C.KOC,C.D.REINKEMEIER, JRNL AUTH 2 E.A.LEMKE,T.STEHLE,D.SCHWARZER JRNL TITL SYNTHESIS, BIOCHEMICAL CHARACTERIZATION, AND GENETIC JRNL TITL 2 ENCODING OF A 1,2,4-TRIAZOLE AMINO ACID AS AN ACETYLLYSINE JRNL TITL 3 MIMIC FOR BROMODOMAINS OF THE BET FAMILY. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 15460 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 36585954 JRNL DOI 10.1002/ANIE.202215460 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 13881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1248 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 36.7300 - 4.0000 1.00 1560 155 0.1862 0.2187 REMARK 3 2 4.0000 - 3.1700 1.00 1459 144 0.1902 0.2223 REMARK 3 3 3.1700 - 2.7700 1.00 1437 142 0.2187 0.2634 REMARK 3 4 2.7700 - 2.5200 1.00 1415 141 0.2058 0.2535 REMARK 3 5 2.5200 - 2.3400 1.00 1404 138 0.2233 0.2496 REMARK 3 6 2.3400 - 2.2000 0.96 1352 134 0.3463 0.3951 REMARK 3 7 2.2000 - 2.0900 0.96 1337 133 0.2588 0.3227 REMARK 3 8 2.0900 - 2.0000 0.99 1387 136 0.2449 0.2509 REMARK 3 9 2.0000 - 1.9200 0.91 1282 125 0.4951 0.4754 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) : 0.289 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.342 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.24 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 : 0.005 988 REMARK 3 ANGLE : 0.632 1339 REMARK 3 CHIRALITY : 0.042 139 REMARK 3 PLANARITY : 0.003 173 REMARK 3 DIHEDRAL : 2.021 810 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -23.5585 -28.1102 3.2375 REMARK 3 T TENSOR REMARK 3 T11: 0.2650 T22: 0.3426 REMARK 3 T33: 0.3273 T12: -0.0122 REMARK 3 T13: -0.0535 T23: -0.0699 REMARK 3 L TENSOR REMARK 3 L11: 1.9358 L22: 3.7798 REMARK 3 L33: 3.9949 L12: -0.0642 REMARK 3 L13: -0.1279 L23: -0.3374 REMARK 3 S TENSOR REMARK 3 S11: 0.1151 S12: -0.1893 S13: -0.0625 REMARK 3 S21: 0.1717 S22: 0.1420 S23: -0.2691 REMARK 3 S31: 0.1114 S32: 0.2856 S33: -0.2307 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 8B5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-18 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99989 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14001 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 25.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 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: 2OO1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM POTASSIUM SODIUM TATRATE 100 MM REMARK 280 SODIUM CITRATE PH 5.6 2 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 31.76667 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 63.53333 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 47.65000 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 79.41667 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 15.88333 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 31.76667 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 63.53333 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 79.41667 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 47.65000 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 15.88333 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: TETRAMERIC 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 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 15.88333 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 506 LIES ON A SPECIAL POSITION. 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 LYS A 307 CG CD CE NZ REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 ARG A 313 CD NE CZ NH1 NH2 REMARK 470 ARG A 320 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 326 CE NZ REMARK 470 LYS A 336 CD CE NZ REMARK 470 LYS A 353 CE NZ REMARK 470 LYS A 362 CE NZ REMARK 470 ARG A 368 CZ NH1 NH2 REMARK 470 LYS A 389 NZ REMARK 470 ARG A 411 CZ NH1 NH2 REMARK 470 HIS B 18 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 19 CD NE CZ NH1 NH2 REMARK 470 ARG B 23 CZ NH1 NH2 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 A 558 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 559 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A 560 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A 561 DISTANCE = 9.41 ANGSTROMS DBREF 8B5A A 307 416 UNP Q15059 BRD3_HUMAN 307 416 DBREF 8B5A B 18 26 PDB 8B5A 8B5A 18 26 SEQRES 1 A 110 LYS LEU SER GLU HIS LEU ARG TYR CYS ASP SER ILE LEU SEQRES 2 A 110 ARG GLU MET LEU SER LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 110 PRO PHE TYR LYS PRO VAL ASP ALA GLU ALA LEU GLU LEU SEQRES 4 A 110 HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP LEU SEQRES 5 A 110 SER THR VAL LYS ARG LYS MET ASP GLY ARG GLU TYR PRO SEQRES 6 A 110 ASP ALA GLN GLY PHE ALA ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 110 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL SEQRES 8 A 110 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET SEQRES 9 A 110 ARG PHE ALA LYS MET PRO SEQRES 1 B 9 HIS ARG P1V VAL LEU ARG ASP ASN TYR HET P1V B 20 14 HETNAM P1V (2~{S})-2-AZANYL-6-(5-METHYL-1~{H}-1,2,4-TRIAZOL-3-YL) HETNAM 2 P1V HEXANOIC ACID FORMUL 2 P1V C9 H16 N4 O2 FORMUL 3 HOH *76(H2 O) HELIX 1 AA1 SER A 309 LEU A 323 1 15 HELIX 2 AA2 SER A 324 LYS A 326 5 3 HELIX 3 AA3 HIS A 327 TRP A 332 1 6 HELIX 4 AA4 PRO A 333 TYR A 335 5 3 HELIX 5 AA5 ASP A 347 ILE A 352 1 6 HELIX 6 AA6 ASP A 357 GLY A 367 1 11 HELIX 7 AA7 ASP A 372 ASN A 391 1 20 HELIX 8 AA8 HIS A 395 LYS A 414 1 20 HELIX 9 AA9 VAL B 21 TYR B 26 5 6 LINK C ARG B 19 N P1V B 20 1555 1555 1.33 LINK C P1V B 20 N VAL B 21 1555 1555 1.33 CRYST1 79.610 79.610 95.300 90.00 90.00 120.00 P 61 2 2 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 0.012561 0.007252 0.000000 0.00000 SCALE2 0.000000 0.014504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010493 0.00000