HEADER GENE REGULATION 09-MAR-21 7EBJ TITLE APO STRUCTURE OF THE MOUSE TRIM66 PHD-BROMO DUAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPARTITE MOTIF-CONTAINING PROTEIN 66; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TRIM66; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE BINDING, PHD FINGER, BROMODOMAIN, EPIGENETICS, GENE KEYWDS 2 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR Z.WANG,J.JIANG REVDAT 3 29-NOV-23 7EBJ 1 REMARK REVDAT 2 05-OCT-22 7EBJ 1 JRNL REVDAT 1 09-MAR-22 7EBJ 0 JRNL AUTH F.ZUO,J.JIANG,H.FU,K.YAN,R.LIEFKE,J.ZHANG,Y.HONG,Z.CHANG, JRNL AUTH 2 N.LIU,Z.WANG,Q.XI JRNL TITL A TRIM66/DAX1/DUX AXIS SUPPRESSES THE TOTIPOTENT 2-CELL-LIKE JRNL TITL 2 STATE IN MURINE EMBRYONIC STEM CELLS. JRNL REF CELL STEM CELL V. 29 948 2022 JRNL REFN ISSN 1875-9777 JRNL PMID 35659877 JRNL DOI 10.1016/J.STEM.2022.05.004 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 24522 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1251 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 46.2200 - 3.7500 0.99 2800 115 0.1782 0.1932 REMARK 3 2 3.7500 - 2.9800 1.00 2613 146 0.1830 0.2038 REMARK 3 3 2.9800 - 2.6000 1.00 2615 140 0.1892 0.2298 REMARK 3 4 2.6000 - 2.3600 1.00 2556 146 0.1806 0.2230 REMARK 3 5 2.3600 - 2.1900 1.00 2586 138 0.1714 0.1956 REMARK 3 6 2.1900 - 2.0600 1.00 2520 137 0.1805 0.2133 REMARK 3 7 2.0600 - 1.9600 0.99 2529 157 0.1885 0.2366 REMARK 3 8 1.9600 - 1.8700 0.99 2520 130 0.1946 0.2199 REMARK 3 9 1.8700 - 1.8000 0.99 2532 142 0.2256 0.2680 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.766 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 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 1429 REMARK 3 ANGLE : 0.855 1935 REMARK 3 CHIRALITY : 0.048 205 REMARK 3 PLANARITY : 0.006 248 REMARK 3 DIHEDRAL : 13.539 537 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 7EBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 77 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24555 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10800 REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 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) : 0.89600 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: 3O33 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE PH 6.5, 12% W/V REMARK 280 POLYETHYLENE GLYCOL 20000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 40.02300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.03650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.03650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.01150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.03650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.03650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.03450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.03650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.03650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.01150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.03650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.03650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.03450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.02300 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 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 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 SER A 991 REMARK 465 PRO A 992 REMARK 465 ILE A 993 REMARK 465 GLU A 994 REMARK 465 ASN A 995 REMARK 465 HIS A 1059 REMARK 465 PRO A 1060 REMARK 465 GLY A 1061 REMARK 465 VAL A 1062 REMARK 465 ARG A 1063 REMARK 465 VAL A 1064 REMARK 465 LEU A 1065 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 GLN A1045 79.16 -118.65 REMARK 500 MET A1048 144.34 -177.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 999 SG REMARK 620 2 CYS A1002 SG 112.6 REMARK 620 3 HIS A1019 ND1 102.2 95.7 REMARK 620 4 CYS A1022 SG 109.9 117.7 117.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1011 SG REMARK 620 2 CYS A1014 SG 113.0 REMARK 620 3 CYS A1037 SG 108.2 111.0 REMARK 620 4 CYS A1040 SG 111.3 102.3 111.1 REMARK 620 N 1 2 3 DBREF 7EBJ A 992 1175 UNP E9PZP2 E9PZP2_MOUSE 992 1175 SEQADV 7EBJ SER A 991 UNP E9PZP2 EXPRESSION TAG SEQRES 1 A 185 SER PRO ILE GLU ASN GLU ASP PHE CYS ALA VAL CYS ILE SEQRES 2 A 185 ASN GLY GLY GLU LEU LEU CYS CYS ASP ARG CYS PRO LYS SEQRES 3 A 185 VAL TYR HIS LEU SER CYS HIS VAL PRO ALA LEU LEU SER SEQRES 4 A 185 PHE PRO GLY GLY GLU TRP VAL CYS THR LEU CYS ARG SER SEQRES 5 A 185 LEU THR GLN PRO GLU MET GLU TYR ASP CYS GLU ASN ALA SEQRES 6 A 185 ARG TYR GLY HIS PRO GLY VAL ARG VAL LEU PRO GLY LEU SEQRES 7 A 185 SER MET TYR ASP GLN LYS LYS CYS GLU LYS LEU VAL LEU SEQRES 8 A 185 SER LEU CYS CYS ASN SER LEU SER LEU PRO PHE HIS GLU SEQRES 9 A 185 PRO VAL SER PRO LEU ALA ARG HIS TYR TYR GLN ILE ILE SEQRES 10 A 185 LYS ARG PRO MET ASP LEU SER ILE ILE ARG ARG LYS LEU SEQRES 11 A 185 GLN LYS LYS ASP PRO ALA HIS TYR THR THR PRO GLU GLU SEQRES 12 A 185 VAL VAL SER ASP VAL ARG LEU MET PHE TRP ASN CYS ALA SEQRES 13 A 185 LYS PHE ASN TYR PRO ASP SER GLU VAL ALA GLU ALA GLY SEQRES 14 A 185 ARG CYS LEU GLU VAL PHE PHE GLU GLY TRP LEU LYS GLU SEQRES 15 A 185 ILE TYR PRO HET ZN A1201 1 HET ZN A1202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *206(H2 O) HELIX 1 AA1 CYS A 1052 GLY A 1058 1 7 HELIX 2 AA2 SER A 1069 ASN A 1086 1 18 HELIX 3 AA3 SER A 1089 GLU A 1094 5 6 HELIX 4 AA4 HIS A 1102 ILE A 1107 1 6 HELIX 5 AA5 ASP A 1112 LEU A 1120 1 9 HELIX 6 AA6 THR A 1130 ASN A 1149 1 20 HELIX 7 AA7 SER A 1153 TYR A 1174 1 22 SHEET 1 AA1 2 LEU A1009 CYS A1010 0 SHEET 2 AA1 2 VAL A1017 TYR A1018 -1 O TYR A1018 N LEU A1009 LINK SG CYS A 999 ZN ZN A1201 1555 1555 2.32 LINK SG CYS A1002 ZN ZN A1201 1555 1555 2.26 LINK SG CYS A1011 ZN ZN A1202 1555 1555 2.33 LINK SG CYS A1014 ZN ZN A1202 1555 1555 2.34 LINK ND1 HIS A1019 ZN ZN A1201 1555 1555 2.16 LINK SG CYS A1022 ZN ZN A1201 1555 1555 2.31 LINK SG CYS A1037 ZN ZN A1202 1555 1555 2.41 LINK SG CYS A1040 ZN ZN A1202 1555 1555 2.25 CISPEP 1 VAL A 1024 PRO A 1025 0 1.75 CRYST1 80.073 80.073 80.046 90.00 90.00 90.00 P 41 21 2 8 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 0.012489 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012489 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012493 0.00000