HEADER TRANSCRIPTION/INHIBITOR 09-OCT-17 5YJ8 TITLE IDENTIFICATION OF A SMALL MOLECULE INHIBITOR FOR THE TUDOR DOMAIN OF TITLE 2 TDRD3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TUDOR DOMAIN; COMPND 5 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: TDRD3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG KEYWDS TRANSCRIPTIONAL COACTIVATOR, COMPLEX, INHIBITOR, TRANSCRIPTION- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,K.RUAN REVDAT 4 22-NOV-23 5YJ8 1 REMARK REVDAT 3 20-JUN-18 5YJ8 1 JRNL REVDAT 2 16-MAY-18 5YJ8 1 JRNL REVDAT 1 02-MAY-18 5YJ8 0 JRNL AUTH J.LIU,S.ZHANG,M.LIU,Y.LIU,G.NSHOGOZA,J.GAO,R.MA,Y.YANG,J.WU, JRNL AUTH 2 J.ZHANG,F.LI,K.RUAN JRNL TITL STRUCTURAL PLASTICITY OF THE TDRD3 TUDOR DOMAIN PROBED BY A JRNL TITL 2 FRAGMENT SCREENING HIT. JRNL REF FEBS J. V. 285 2091 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 29645362 JRNL DOI 10.1111/FEBS.14469 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 6480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 635 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 1.8982 - 1.7621 0.00 1227 132 0.1876 0.2248 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) : 24.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.59 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 549 THROUGH 560 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.2559 25.1995 1.4155 REMARK 3 T TENSOR REMARK 3 T11: 0.2014 T22: 0.2465 REMARK 3 T33: 0.1632 T12: -0.0274 REMARK 3 T13: -0.0010 T23: 0.0187 REMARK 3 L TENSOR REMARK 3 L11: 3.6418 L22: 3.4288 REMARK 3 L33: 1.8732 L12: -3.5104 REMARK 3 L13: 0.9593 L23: -1.1963 REMARK 3 S TENSOR REMARK 3 S11: 0.1102 S12: -0.1652 S13: 0.2561 REMARK 3 S21: -0.0123 S22: -0.1323 S23: -0.3552 REMARK 3 S31: 0.0136 S32: 0.1990 S33: 0.0582 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 561 THROUGH 570 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6527 17.5672 2.6664 REMARK 3 T TENSOR REMARK 3 T11: 0.2099 T22: 0.2813 REMARK 3 T33: 0.2138 T12: 0.0058 REMARK 3 T13: 0.0357 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 8.9410 L22: 2.1397 REMARK 3 L33: 3.7759 L12: 1.0669 REMARK 3 L13: 1.6676 L23: -0.0168 REMARK 3 S TENSOR REMARK 3 S11: -0.2819 S12: 0.4565 S13: 0.5681 REMARK 3 S21: -0.0498 S22: 0.1589 S23: -0.1753 REMARK 3 S31: -0.1553 S32: 0.5453 S33: 0.1046 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 571 THROUGH 595 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1714 15.4341 5.5858 REMARK 3 T TENSOR REMARK 3 T11: 0.2059 T22: 0.2351 REMARK 3 T33: 0.1846 T12: -0.0099 REMARK 3 T13: -0.0268 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 7.8424 L22: 3.2343 REMARK 3 L33: 4.8760 L12: -2.0991 REMARK 3 L13: -1.5423 L23: 0.8960 REMARK 3 S TENSOR REMARK 3 S11: -0.1201 S12: 0.3899 S13: 0.1092 REMARK 3 S21: -0.0466 S22: -0.0966 S23: -0.0399 REMARK 3 S31: 0.1293 S32: -0.0105 S33: 0.1851 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 596 THROUGH 608 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.2368 19.0161 4.9429 REMARK 3 T TENSOR REMARK 3 T11: 0.1805 T22: 0.2397 REMARK 3 T33: 0.3085 T12: 0.0100 REMARK 3 T13: 0.0190 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 3.0611 L22: 4.0293 REMARK 3 L33: 3.1875 L12: -1.1258 REMARK 3 L13: 2.8781 L23: -0.6218 REMARK 3 S TENSOR REMARK 3 S11: -0.1899 S12: 0.2497 S13: 0.4687 REMARK 3 S21: 0.1259 S22: -0.1224 S23: -0.2124 REMARK 3 S31: -0.2345 S32: 0.2185 S33: 0.3305 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 5YJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 0.9774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6495 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 15.70 REMARK 200 R MERGE FOR SHELL (I) : 0.50400 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: 3PMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE TRIHYDRATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 28.05800 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 14.02900 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 14.02900 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 28.05800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 S SO4 A 702 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 837 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 838 LIES ON A SPECIAL POSITION. 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 ASP A 569 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8W9 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 702 DBREF 5YJ8 A 555 608 UNP Q9H7E2 TDRD3_HUMAN 555 608 SEQADV 5YJ8 HIS A 549 UNP Q9H7E2 EXPRESSION TAG SEQADV 5YJ8 HIS A 550 UNP Q9H7E2 EXPRESSION TAG SEQADV 5YJ8 HIS A 551 UNP Q9H7E2 EXPRESSION TAG SEQADV 5YJ8 HIS A 552 UNP Q9H7E2 EXPRESSION TAG SEQADV 5YJ8 HIS A 553 UNP Q9H7E2 EXPRESSION TAG SEQADV 5YJ8 MET A 554 UNP Q9H7E2 EXPRESSION TAG SEQRES 1 A 60 HIS HIS HIS HIS HIS MET MET TRP LYS PRO GLY ASP GLU SEQRES 2 A 60 CYS PHE ALA LEU TYR TRP GLU ASP ASN LYS PHE TYR ARG SEQRES 3 A 60 ALA GLU VAL GLU ALA LEU HIS SER SER GLY MET THR ALA SEQRES 4 A 60 VAL VAL LYS PHE ILE ASP TYR GLY ASN TYR GLU GLU VAL SEQRES 5 A 60 LEU LEU SER ASN ILE LYS PRO ILE HET 8W9 A 701 14 HET SO4 A 702 5 HETNAM 8W9 5-(AMINOMETHYL)-1,3-DIMETHYL-BENZIMIDAZOL-2-ONE HETNAM SO4 SULFATE ION FORMUL 2 8W9 C10 H13 N3 O FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *38(H2 O) HELIX 1 AA1 HIS A 549 HIS A 553 5 5 SHEET 1 AA1 5 TYR A 597 LEU A 601 0 SHEET 2 AA1 5 THR A 586 PHE A 591 -1 N VAL A 589 O GLU A 598 SHEET 3 AA1 5 PHE A 572 HIS A 581 -1 N GLU A 578 O VAL A 588 SHEET 4 AA1 5 GLU A 561 LEU A 565 -1 N CYS A 562 O ALA A 575 SHEET 5 AA1 5 ILE A 605 PRO A 607 -1 O LYS A 606 N PHE A 563 SITE 1 AC1 6 HIS A 550 TYR A 566 TYR A 573 PHE A 591 SITE 2 AC1 6 TYR A 594 ASN A 596 SITE 1 AC2 4 HIS A 549 HIS A 550 HIS A 551 HOH A 819 CRYST1 50.974 50.974 42.087 90.00 90.00 120.00 P 32 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 0.019618 0.011326 0.000000 0.00000 SCALE2 0.000000 0.022653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023760 0.00000