HEADER PEPTIDE BINDING PROTEIN 22-SEP-22 8B5C TITLE HUMAN BRD4 BROMDOMAIN 1 IN COMPLEX WITH A H4 PEPTIDE CONTAINING APMTRI TITLE 2 (H4K5/8APMTRI) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HUNK1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: H4K5/8APMTRI; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: NON-NATURAL AMINO ACID APMTRI CONTAINING H4 PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BRD4, HUNK1; 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 8B5C 1 LINK REVDAT 5 24-MAY-23 8B5C 1 FORMUL REVDAT 4 22-MAR-23 8B5C 1 JRNL REVDAT 3 15-MAR-23 8B5C 1 JRNL REVDAT 2 15-FEB-23 8B5C 1 JRNL REVDAT 1 11-JAN-23 8B5C 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. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16698 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1503 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 36.6200 - 3.5100 1.00 1496 148 0.1691 0.1752 REMARK 3 2 3.5100 - 2.7800 1.00 1402 139 0.1707 0.1888 REMARK 3 3 2.7800 - 2.4300 1.00 1399 138 0.1780 0.2126 REMARK 3 4 2.4300 - 2.2100 1.00 1376 136 0.1671 0.1902 REMARK 3 5 2.2100 - 2.0500 1.00 1381 137 0.1661 0.2107 REMARK 3 6 2.0500 - 1.9300 1.00 1365 135 0.1797 0.1923 REMARK 3 7 1.9300 - 1.8300 1.00 1368 135 0.1902 0.2191 REMARK 3 8 1.8300 - 1.7500 1.00 1357 135 0.2159 0.2980 REMARK 3 9 1.7500 - 1.6900 1.00 1364 135 0.2695 0.2926 REMARK 3 10 1.6900 - 1.6300 1.00 1349 133 0.2647 0.3119 REMARK 3 11 1.6300 - 1.5800 1.00 1338 132 0.3059 0.3287 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) : 0.189 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.57 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 1130 REMARK 3 ANGLE : 0.898 1538 REMARK 3 CHIRALITY : 0.047 164 REMARK 3 PLANARITY : 0.006 196 REMARK 3 DIHEDRAL : 2.930 941 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): -7.5201 7.8069 -16.6647 REMARK 3 T TENSOR REMARK 3 T11: 0.1492 T22: 0.1504 REMARK 3 T33: 0.1485 T12: -0.0020 REMARK 3 T13: -0.0092 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 0.1601 L22: 0.2476 REMARK 3 L33: 0.1402 L12: 0.1493 REMARK 3 L13: 0.0119 L23: 0.0059 REMARK 3 S TENSOR REMARK 3 S11: 0.0094 S12: -0.0445 S13: -0.0808 REMARK 3 S21: 0.0288 S22: -0.0196 S23: 0.0000 REMARK 3 S31: 0.0023 S32: 0.0029 S33: 0.0000 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 8B5C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292124763. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.999867 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 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: PHASER REMARK 200 STARTING MODEL: 2OSS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM ACETATE TRIHYDRATE 100 REMARK 280 MM TRISHYDROCHLORIDE PH 8.5 30% W/V PEG 4000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.26350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.45100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.37400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.45100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.26350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.37400 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 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 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 GLU A 167 REMARK 465 GLU A 168 REMARK 465 GLY B 11 REMARK 465 LYS B 12 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 GLY A 40 N CA REMARK 470 ASN A 52 CG OD1 ND2 REMARK 470 GLN A 59 CG CD OE1 NE2 REMARK 470 ASN A 61 CG OD1 ND2 REMARK 470 GLN A 64 CG CD OE1 NE2 REMARK 470 ARG A 68 NE CZ NH1 NH2 REMARK 470 LYS A 76 CE NZ REMARK 470 GLN A 78 CG CD OE1 NE2 REMARK 470 LYS A 99 CE NZ REMARK 470 GLN A 123 CG CD OE1 NE2 REMARK 470 GLN A 127 CD OE1 NE2 REMARK 470 LYS A 141 CD CE NZ REMARK 470 THR A 166 OG1 CG2 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 69 -56.86 -123.93 REMARK 500 REMARK 500 REMARK: NULL 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 274 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 275 DISTANCE = 6.70 ANGSTROMS DBREF 8B5C A 44 168 UNP O60885 BRD4_HUMAN 44 168 DBREF 8B5C B 0 12 PDB 8B5C 8B5C 0 12 SEQADV 8B5C GLY A 40 UNP O60885 EXPRESSION TAG SEQADV 8B5C SER A 41 UNP O60885 EXPRESSION TAG SEQADV 8B5C HIS A 42 UNP O60885 EXPRESSION TAG SEQADV 8B5C MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 129 GLY SER HIS MET ASN PRO PRO PRO PRO GLU THR SER ASN SEQRES 2 A 129 PRO ASN LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR SEQRES 3 A 129 LEU LEU ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN SEQRES 4 A 129 PHE ALA TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS SEQRES 5 A 129 LEU ASN LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO SEQRES 6 A 129 MET ASP MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN SEQRES 7 A 129 TYR TYR TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN SEQRES 8 A 129 THR MET PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY SEQRES 9 A 129 ASP ASP ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU SEQRES 10 A 129 PHE LEU GLN LYS ILE ASN GLU LEU PRO THR GLU GLU SEQRES 1 B 13 ACE SER GLY ARG GLY P1V GLY GLY P1V GLY LEU GLY LYS HET ACE B 0 3 HET P1V B 5 14 HET P1V B 8 14 HETNAM ACE ACETYL GROUP HETNAM P1V (2~{S})-2-AZANYL-6-(5-METHYL-1~{H}-1,2,4-TRIAZOL-3-YL) HETNAM 2 P1V HEXANOIC ACID FORMUL 2 ACE C2 H4 O FORMUL 2 P1V 2(C9 H16 N4 O2) FORMUL 3 HOH *78(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 LYS A 76 1 8 HELIX 3 AA3 ALA A 80 GLN A 84 5 5 HELIX 4 AA4 ASP A 96 ILE A 101 1 6 HELIX 5 AA5 ASP A 106 ASN A 116 1 11 HELIX 6 AA6 ASN A 121 ASN A 140 1 20 HELIX 7 AA7 ASP A 144 ASN A 162 1 19 LINK C ACE B 0 N SER B 1 1555 1555 1.33 LINK C GLY B 4 N P1V B 5 1555 1555 1.33 LINK C P1V B 5 N GLY B 6 1555 1555 1.33 LINK C GLY B 7 N P1V B 8 1555 1555 1.33 LINK C P1V B 8 N GLY B 9 1555 1555 1.33 CRYST1 42.527 46.748 58.902 90.00 90.00 90.00 P 21 21 21 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 0.023514 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016977 0.00000