HEADER DNA BINDING PROTEIN 03-JAN-18 5Z2S TITLE CRYSTAL STRUCTURE OF DUX4-HD2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE HOMEOBOX PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DOUBLE HOMEOBOX PROTEIN 10; 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: DUX4, DUX10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACUTE LYMPHOBLASTIC LEUKEMIA, DUX4/IGH, DUX4-RESPONSIVE-ELEMENT, KEYWDS 2 TRANSACTIVATION, ERGALT, DNA BINDING PROTEIN 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 5Z2S 1 REMARK REVDAT 2 20-JUN-18 5Z2S 1 JRNL REVDAT 1 04-APR-18 5Z2S 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 7442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 361 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 23.9686 - 2.1630 0.83 2151 118 0.1991 0.2434 REMARK 3 2 2.1630 - 1.7170 1.00 2472 137 0.1830 0.1756 REMARK 3 3 1.5800 - 1.5000 1.00 2458 106 0.1754 0.2244 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.820 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 : 0.010 414 REMARK 3 ANGLE : 1.127 556 REMARK 3 CHIRALITY : 0.050 59 REMARK 3 PLANARITY : 0.006 74 REMARK 3 DIHEDRAL : 11.058 253 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.6834 17.8166 -12.0892 REMARK 3 T TENSOR REMARK 3 T11: 0.0272 T22: 0.0360 REMARK 3 T33: 0.0197 T12: 0.0006 REMARK 3 T13: 0.0304 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.0269 L22: 0.0041 REMARK 3 L33: 0.0063 L12: -0.0088 REMARK 3 L13: -0.0091 L23: 0.0019 REMARK 3 S TENSOR REMARK 3 S11: 0.0135 S12: 0.0685 S13: -0.0111 REMARK 3 S21: 0.0050 S22: -0.0006 S23: 0.0251 REMARK 3 S31: -0.0316 S32: -0.0577 S33: -0.0008 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1089 17.2273 -11.3229 REMARK 3 T TENSOR REMARK 3 T11: 0.0334 T22: 0.0316 REMARK 3 T33: 0.0372 T12: 0.0080 REMARK 3 T13: 0.0067 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 0.0334 L22: 0.0353 REMARK 3 L33: 0.0618 L12: -0.0107 REMARK 3 L13: 0.0350 L23: -0.0368 REMARK 3 S TENSOR REMARK 3 S11: -0.0301 S12: 0.0519 S13: -0.0165 REMARK 3 S21: 0.0474 S22: 0.0334 S23: -0.0479 REMARK 3 S31: -0.0039 S32: 0.0020 S33: -0.0134 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 54 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2702 9.2876 -8.3581 REMARK 3 T TENSOR REMARK 3 T11: 0.0503 T22: 0.0324 REMARK 3 T33: 0.0415 T12: -0.0035 REMARK 3 T13: -0.0024 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.0228 L22: 0.0146 REMARK 3 L33: 0.0781 L12: -0.0084 REMARK 3 L13: 0.0347 L23: 0.0032 REMARK 3 S TENSOR REMARK 3 S11: -0.0325 S12: -0.0605 S13: -0.0457 REMARK 3 S21: 0.0236 S22: 0.0586 S23: 0.0085 REMARK 3 S31: -0.0120 S32: -0.0678 S33: 0.0017 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 5Z2S 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_1300006375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-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) : 0.9792 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 : 7483 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 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) : 1.58 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: 3A02 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 273K 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 12.57500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.28500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.28500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.57500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 12.69500 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: 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 PRO A 55 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 NZ LYS A 20 O HOH A 101 1.93 REMARK 500 O HOH A 179 O HOH A 206 2.08 REMARK 500 O HOH A 101 O HOH A 170 2.09 REMARK 500 NH1 ARG A 34 O HOH A 102 2.12 REMARK 500 O HOH A 158 O HOH A 203 2.14 REMARK 500 O HOH A 177 O HOH A 194 2.16 REMARK 500 N ALA A 5 O HOH A 103 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 112 O HOH A 182 3654 2.14 REMARK 500 O HOH A 201 O HOH A 204 1455 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 5Z2S A 5 55 UNP Q9UBX2 DUX4_HUMAN 100 150 SEQADV 5Z2S GLY A 1 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2S SER A 2 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2S HIS A 3 UNP Q9UBX2 EXPRESSION TAG SEQADV 5Z2S MET A 4 UNP Q9UBX2 EXPRESSION TAG SEQRES 1 A 55 GLY SER HIS MET ALA VAL THR GLY SER GLN THR ALA LEU SEQRES 2 A 55 LEU LEU ARG ALA PHE GLU LYS ASP ARG PHE PRO GLY ILE SEQRES 3 A 55 ALA ALA ARG GLU GLU LEU ALA ARG GLU THR GLY LEU PRO SEQRES 4 A 55 GLU SER ARG ILE GLN ILE TRP PHE GLN ASN ARG ARG ALA SEQRES 5 A 55 ARG HIS PRO FORMUL 2 HOH *108(H2 O) HELIX 1 AA1 THR A 7 GLU A 19 1 13 HELIX 2 AA2 GLY A 25 GLY A 37 1 13 HELIX 3 AA3 PRO A 39 HIS A 54 1 16 CRYST1 25.150 25.390 72.570 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 0.039761 0.000000 0.000000 0.00000 SCALE2 0.000000 0.039386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013780 0.00000