HEADER DNA BINDING PROTEIN/DNA 04-JAN-18 5Z2T TITLE CRYSTAL STRUCTURE OF DNA-BOUND DUX4-HD2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE HOMEOBOX PROTEIN 4; COMPND 3 CHAIN: C, D; COMPND 4 SYNONYM: DOUBLE HOMEOBOX PROTEIN 10; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*TP*T)-3'; COMPND 8 CHAIN: E; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(P*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3'; COMPND 12 CHAIN: F; COMPND 13 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: DUX4, DUX10; 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: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS ACUTE LYMPHOBLASTIC LEUKEMIA, DUX4/IGH, DUX4-RESPONSIVE-ELEMENT, KEYWDS 2 TRANSACTIVATION, ERGALT, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.DONG,W.ZHANG,H.WU,J.HUANG,M.ZHANG,P.WANG,H.ZHANG,Z.CHEN,S.CHEN, AUTHOR 2 G.MENG REVDAT 3 22-NOV-23 5Z2T 1 REMARK REVDAT 2 20-JUN-18 5Z2T 1 JRNL REVDAT 1 04-APR-18 5Z2T 0 JRNL AUTH X.DONG,W.ZHANG,H.WU,J.HUANG,M.ZHANG,P.WANG,H.ZHANG,Z.CHEN, JRNL AUTH 2 S.J.CHEN,G.MENG JRNL TITL STRUCTURAL BASIS OF DUX4/IGH-DRIVEN TRANSACTIVATION. JRNL REF LEUKEMIA V. 32 1466 2018 JRNL REFN ESSN 1476-5551 JRNL PMID 29572508 JRNL DOI 10.1038/S41375-018-0093-1 REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 7266 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.278 REMARK 3 R VALUE (WORKING SET) : 0.276 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 341 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 49.3061 - 3.3047 0.99 3565 176 0.2511 0.2685 REMARK 3 2 2.7600 - 2.6200 0.99 3360 165 0.3726 0.4284 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.710 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 : 0.005 1480 REMARK 3 ANGLE : 0.826 2104 REMARK 3 CHIRALITY : 0.039 230 REMARK 3 PLANARITY : 0.005 185 REMARK 3 DIHEDRAL : 26.004 797 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): 24.8174 0.9616 185.1903 REMARK 3 T TENSOR REMARK 3 T11: 0.3118 T22: 0.4535 REMARK 3 T33: 0.3680 T12: -0.1134 REMARK 3 T13: -0.0109 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 0.7603 L22: 1.1733 REMARK 3 L33: 0.9139 L12: -0.5851 REMARK 3 L13: 0.0614 L23: 0.2112 REMARK 3 S TENSOR REMARK 3 S11: 0.0036 S12: -0.1651 S13: -0.0562 REMARK 3 S21: -0.2114 S22: 0.1141 S23: -0.0443 REMARK 3 S31: -0.0031 S32: 0.0458 S33: 0.0002 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 5Z2T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006374. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-16 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9747 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7363 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 83.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 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: 5Z2S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 273K 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 83.27500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.80500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.80500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.63750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.80500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.80500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 124.91250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.80500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.80500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.63750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.80500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.80500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 124.91250 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 83.27500 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: C, E, F, D 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 C 1 REMARK 465 SER C 2 REMARK 465 HIS C 3 REMARK 465 MET C 4 REMARK 465 GLY C 5 REMARK 465 ARG C 6 REMARK 465 ARG C 7 REMARK 465 LYS C 8 REMARK 465 GLY C 62 REMARK 465 GLN C 63 REMARK 465 GLY C 64 REMARK 465 DT E 0 REMARK 465 DT E 1 REMARK 465 DT F 27 REMARK 465 GLY D 1 REMARK 465 SER D 2 REMARK 465 HIS D 3 REMARK 465 MET D 4 REMARK 465 GLY D 5 REMARK 465 ARG D 6 REMARK 465 ARG D 7 REMARK 465 LYS D 8 REMARK 465 GLN D 63 REMARK 465 GLY D 64 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 O2 DC E 2 N2 DG F 26 1.98 REMARK 500 OP2 DG F 26 O HOH F 101 2.08 REMARK 500 O HOH E 102 O HOH D 104 2.09 REMARK 500 OP2 DA F 17 O HOH F 102 2.11 REMARK 500 OP2 DT E 13 O HOH E 101 2.13 REMARK 500 OG1 THR D 10 O HOH D 101 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 HIS C 60 70.99 -163.40 REMARK 500 THR D 10 -140.17 -154.27 REMARK 500 ALA D 11 69.03 74.31 REMARK 500 HIS D 60 74.93 -171.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 5Z2T C 5 64 UNP Q9UBX2 DUX4_HUMAN 94 153 DBREF 5Z2T E 0 14 PDB 5Z2T 5Z2T 0 14 DBREF 5Z2T F 14 27 PDB 5Z2T 5Z2T 14 27 DBREF 5Z2T D 5 64 UNP Q9UBX2 DUX4_HUMAN 94 153 SEQADV 5Z2T GLY C 1 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2T SER C 2 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2T HIS C 3 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2T MET C 4 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2T GLY D 1 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2T SER D 2 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2T HIS D 3 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2T MET D 4 UNP Q9UBX2 EXPRESSION TAG SEQRES 1 C 64 GLY SER HIS MET GLY ARG ARG LYS ARG THR ALA VAL THR SEQRES 2 C 64 GLY SER GLN THR ALA LEU LEU LEU ARG ALA PHE GLU LYS SEQRES 3 C 64 ASP ARG PHE PRO GLY ILE ALA ALA ARG GLU GLU LEU ALA SEQRES 4 C 64 ARG GLU THR GLY LEU PRO GLU SER ARG ILE GLN ILE TRP SEQRES 5 C 64 PHE GLN ASN ARG ARG ALA ARG HIS PRO GLY GLN GLY SEQRES 1 E 15 DT DT DC DT DA DA DT DC DT DA DA DT DC SEQRES 2 E 15 DT DT SEQRES 1 F 14 DA DA DG DA DT DT DA DG DA DT DT DA DG SEQRES 2 F 14 DT SEQRES 1 D 64 GLY SER HIS MET GLY ARG ARG LYS ARG THR ALA VAL THR SEQRES 2 D 64 GLY SER GLN THR ALA LEU LEU LEU ARG ALA PHE GLU LYS SEQRES 3 D 64 ASP ARG PHE PRO GLY ILE ALA ALA ARG GLU GLU LEU ALA SEQRES 4 D 64 ARG GLU THR GLY LEU PRO GLU SER ARG ILE GLN ILE TRP SEQRES 5 D 64 PHE GLN ASN ARG ARG ALA ARG HIS PRO GLY GLN GLY FORMUL 5 HOH *11(H2 O) HELIX 1 AA1 THR C 13 ASP C 27 1 15 HELIX 2 AA2 GLY C 31 GLY C 43 1 13 HELIX 3 AA3 PRO C 45 HIS C 60 1 16 HELIX 4 AA4 THR D 13 ASP D 27 1 15 HELIX 5 AA5 GLY D 31 GLY D 43 1 13 HELIX 6 AA6 PRO D 45 HIS D 60 1 16 CRYST1 51.610 51.610 166.550 90.00 90.00 90.00 P 41 21 2 16 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 0.019376 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019376 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006004 0.00000