HEADER PROTEIN BINDING 17-SEP-18 6IEW TITLE THE CRYSTAL STRUCTURE OF THE DNXF2 UBA DOMAIN IN COMPLEX WITH TITLE 2 PANORAMIX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUSION PROTEIN OF NUCLEAR RNA EXPORT FACTOR 2 AND PROTEIN COMPND 3 PANORAMIX; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PROTEIN SILENCIO; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: NXF2, CG4118, PANX, CG9754; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PIRNA, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.HUANG,S.CHENG REVDAT 3 27-MAR-24 6IEW 1 REMARK REVDAT 2 26-FEB-20 6IEW 1 JRNL REVDAT 1 21-AUG-19 6IEW 0 JRNL AUTH K.ZHAO,S.CHENG,N.MIAO,P.XU,X.LU,Y.ZHANG,M.WANG,X.OUYANG, JRNL AUTH 2 X.YUAN,W.LIU,X.LU,P.ZHOU,J.GU,Y.ZHANG,D.QIU,Z.JIN,C.SU, JRNL AUTH 3 C.PENG,J.H.WANG,M.Q.DONG,Y.WAN,J.MA,H.CHENG,Y.HUANG,Y.YU JRNL TITL A PANDAS COMPLEX ADAPTED FOR PIRNA-GUIDED TRANSCRIPTIONAL JRNL TITL 2 SILENCING AND HETEROCHROMATIN FORMATION. JRNL REF NAT.CELL BIOL. V. 21 1261 2019 JRNL REFN ISSN 1465-7392 JRNL PMID 31570835 JRNL DOI 10.1038/S41556-019-0396-0 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 16378 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1638 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 29.0795 - 3.4318 1.00 1350 150 0.1659 0.1671 REMARK 3 2 3.4318 - 2.7246 1.00 1273 142 0.1649 0.1674 REMARK 3 3 2.7246 - 2.3803 1.00 1251 139 0.1710 0.1564 REMARK 3 4 2.3803 - 2.1628 1.00 1245 138 0.1536 0.1710 REMARK 3 5 2.1628 - 2.0078 1.00 1235 137 0.1482 0.1621 REMARK 3 6 2.0078 - 1.8894 1.00 1232 137 0.1679 0.2004 REMARK 3 7 1.8894 - 1.7948 1.00 1213 135 0.1669 0.2032 REMARK 3 8 1.7948 - 1.7167 1.00 1221 136 0.1631 0.1705 REMARK 3 9 1.7167 - 1.6506 1.00 1234 137 0.1562 0.1718 REMARK 3 10 1.6506 - 1.5937 1.00 1220 136 0.1583 0.1890 REMARK 3 11 1.5937 - 1.5439 0.97 1165 129 0.1727 0.1991 REMARK 3 12 1.5439 - 1.4997 0.89 1101 122 0.1860 0.2123 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 748 REMARK 3 ANGLE : 0.640 1011 REMARK 3 CHIRALITY : 0.056 116 REMARK 3 PLANARITY : 0.003 129 REMARK 3 DIHEDRAL : 13.001 284 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 6IEW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300009073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-17 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 : 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) : 0.9778 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-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16378 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%(W/V) PEG3350, 0.1M TRIS (PH 9.0), REMARK 280 0.2M SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.46250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.54550 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.46250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.54550 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: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 851 REMARK 465 SER A 852 REMARK 465 GLY A 853 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1125 O HOH A 1156 1.87 REMARK 500 O HOH A 1237 O HOH A 1256 1.94 REMARK 500 O HOH A 1106 O HOH A 1238 1.94 REMARK 500 O HOH A 1257 O HOH A 1272 2.01 REMARK 500 O SER A 850 O HOH A 1101 2.03 REMARK 500 O HOH A 1246 O HOH A 1298 2.04 REMARK 500 O HOH A 1241 O HOH A 1282 2.09 REMARK 500 O HOH A 1201 O HOH A 1282 2.16 REMARK 500 O HOH A 1195 O HOH A 1235 2.16 REMARK 500 O HOH A 1208 O HOH A 1278 2.19 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 A1316 DISTANCE = 7.13 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1000 DBREF 6IEW A 793 846 UNP Q9VV73 NXF2_DROME 788 841 DBREF 6IEW A 315 341 UNP Q9W2H9 PANX_DROME 315 341 SEQADV 6IEW GLY A 788 UNP Q9VV73 EXPRESSION TAG SEQADV 6IEW PRO A 789 UNP Q9VV73 EXPRESSION TAG SEQADV 6IEW LEU A 790 UNP Q9VV73 EXPRESSION TAG SEQADV 6IEW GLY A 791 UNP Q9VV73 EXPRESSION TAG SEQADV 6IEW SER A 792 UNP Q9VV73 EXPRESSION TAG SEQADV 6IEW GLY A 847 UNP Q9VV73 LINKER SEQADV 6IEW SER A 848 UNP Q9VV73 LINKER SEQADV 6IEW GLY A 849 UNP Q9VV73 LINKER SEQADV 6IEW SER A 850 UNP Q9VV73 LINKER SEQADV 6IEW GLY A 851 UNP Q9VV73 LINKER SEQADV 6IEW SER A 852 UNP Q9VV73 LINKER SEQADV 6IEW GLY A 853 UNP Q9VV73 LINKER SEQADV 6IEW SER A 854 UNP Q9VV73 LINKER SEQRES 1 A 94 GLY PRO LEU GLY SER ASP VAL LYS ASP HIS LYS LEU LEU SEQRES 2 A 94 LEU PHE GLN GLU VAL THR GLY LEU ILE SER THR TRP VAL SEQRES 3 A 94 THR SER ILE VAL GLU GLU ALA ASP TRP ASP PHE GLU ARG SEQRES 4 A 94 ALA LEU LYS LEU PHE ILE GLN LYS ASN ALA ASP HIS GLU SEQRES 5 A 94 ILE PRO ASP LEU ALA PHE ALA GLY SER GLY SER GLY SER SEQRES 6 A 94 GLY SER LEU SER LYS ALA ASP LYS ARG SER LEU ALA VAL SEQRES 7 A 94 ALA ARG ALA GLU LEU VAL LEU GLU GLN ILE GLN GLN LYS SEQRES 8 A 94 ALA ASN LYS HET GOL A1000 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *216(H2 O) HELIX 1 AA1 LEU A 790 GLY A 807 1 18 HELIX 2 AA2 ILE A 809 ALA A 820 1 12 HELIX 3 AA3 ASP A 823 ASP A 837 1 15 HELIX 4 AA4 PRO A 841 PHE A 845 5 5 HELIX 5 AA5 SER A 316 LYS A 341 1 26 SITE 1 AC1 7 ARG A 327 GLU A 804 HOH A1112 HOH A1132 SITE 2 AC1 7 HOH A1180 HOH A1199 HOH A1221 CRYST1 29.074 40.925 83.091 90.00 90.00 90.00 P 2 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 0.034395 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012035 0.00000