PDB Short entry for 5ZJS HEADER TRANSCRIPTION/DNA 22-MAR-18 5ZJS TITLE STRUCTURE OF ABDB/EXD COMPLEX BOUND TO A 'BLUE14' DNA SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN ABDOMINAL-B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INFRAABDOMINAL 7,IAB-7,P3,PH189; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HOMEOBOX PROTEIN EXTRADENTICLE; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: DPBX; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*TP*TP*AP*AP*TP*CP*AP*TP*GP*C)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*AP*AP*TP*GP*AP*C)-3'); COMPND 17 CHAIN: D; COMPND 18 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: ABD-B, CG10291; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 10 ORGANISM_COMMON: FRUIT FLY; SOURCE 11 ORGANISM_TAXID: 7227; SOURCE 12 GENE: EXD, CG8933; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 18 ORGANISM_TAXID: 7227; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 22 ORGANISM_TAXID: 7227 KEYWDS ABDB, EXD, DNA, SHAPE, SPECIFICITY, HOX, HOMEODOMAIN, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.BABURAJENDRAN,T.ZEISKE,A.KACZYNSKA,R.MANN,B.HONIG,L.SHAPIRO, AUTHOR 2 A.G.PALMER REVDAT 4 22-NOV-23 5ZJS 1 REMARK REVDAT 3 19-SEP-18 5ZJS 1 AUTHOR JRNL REVDAT 2 12-SEP-18 5ZJS 1 JRNL REVDAT 1 29-AUG-18 5ZJS 0 JRNL AUTH T.ZEISKE,N.BABURAJENDRAN,A.KACZYNSKA,J.BRASCH,A.G.PALMER, JRNL AUTH 2 L.SHAPIRO,B.HONIG,R.S.MANN JRNL TITL INTRINSIC DNA SHAPE ACCOUNTS FOR AFFINITY DIFFERENCES JRNL TITL 2 BETWEEN HOX-COFACTOR BINDING SITES. JRNL REF CELL REP V. 24 2221 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 30157419 JRNL DOI 10.1016/J.CELREP.2018.07.100 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 7436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 343 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 28.1447 - 3.6471 0.95 3642 180 0.2460 0.2692 REMARK 3 2 3.6471 - 2.8957 0.92 3451 163 0.2690 0.3099 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.79 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 : 0.004 1673 REMARK 3 ANGLE : 0.697 2380 REMARK 3 CHIRALITY : 0.029 257 REMARK 3 PLANARITY : 0.002 210 REMARK 3 DIHEDRAL : 25.139 633 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): -17.9431 2.2398 122.0441 REMARK 3 T TENSOR REMARK 3 T11: 0.3138 T22: 0.3293 REMARK 3 T33: 0.3727 T12: -0.0756 REMARK 3 T13: 0.0036 T23: -0.0194 REMARK 3 L TENSOR REMARK 3 L11: 1.4030 L22: 0.6740 REMARK 3 L33: 1.3968 L12: -0.1435 REMARK 3 L13: -0.7476 L23: -0.2397 REMARK 3 S TENSOR REMARK 3 S11: -0.1831 S12: 0.3474 S13: 0.1425 REMARK 3 S21: -0.2013 S22: 0.1786 S23: 0.0386 REMARK 3 S31: 0.1249 S32: 0.2114 S33: 0.0366 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 5ZJS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300007151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-14 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7524 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.896 REMARK 200 RESOLUTION RANGE LOW (A) : 28.143 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 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 <I/SIGMA(I)> 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: 5ZJQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM MGCL2, 0.1M TRIS PH 5.8, 17.5% REMARK 280 PEG 3350, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 38.88000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.82900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.88000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.82900 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 VAL A 1 REMARK 465 GLY A 2 REMARK 465 PRO A 3 REMARK 465 CYS A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 ASN A 7 REMARK 465 PRO A 8 REMARK 465 GLY A 9 REMARK 465 LEU A 10 REMARK 465 HIS A 11 REMARK 465 GLU A 12 REMARK 465 THR A 14 REMARK 465 GLY A 15 REMARK 465 GLN A 16 REMARK 465 VAL A 17 REMARK 465 SER A 18 REMARK 465 VAL A 19 REMARK 465 ARG A 20 REMARK 465 SER A 78 REMARK 465 GLN A 79 REMARK 465 ARG A 80 REMARK 465 GLN A 81 REMARK 465 ALA A 82 REMARK 465 ASN A 83 REMARK 465 GLN A 84 REMARK 465 ASP B 1 REMARK 465 ALA B 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 24 CG CD CE NZ REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 ARG B 3 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 4 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 5 CG CD CE NZ REMARK 470 ARG B 7 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 SER B 23 OG REMARK 470 LEU B 25 CG CD1 CD2 REMARK 470 SER B 26 OG REMARK 470 ASN B 27 CG OD1 ND2 REMARK 470 SER B 31 OG REMARK 470 GLU B 32 CG CD OE1 OE2 REMARK 470 GLU B 33 CG CD OE1 OE2 REMARK 470 LYS B 35 CG CD CE NZ REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 ARG B 40 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 ILE B 44 CG1 CG2 CD1 REMARK 470 ARG B 57 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 ASN B 63 CG OD1 ND2 REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU B 69 CG CD OE1 OE2 REMARK 470 GLU B 70 CG CD OE1 OE2 REMARK 470 TYR B 74 CG CD1 CD2 CE1 CE2 CZ OH 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 OH TYR B 29 OP1 DT C 6 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 5ZJS A 1 84 UNP P09087 ABDB_DROME 369 452 DBREF 5ZJS B 1 74 UNP P40427 EXD_DROME 237 310 DBREF 5ZJS C 1 14 PDB 5ZJS 5ZJS 1 14 DBREF 5ZJS D 1 14 PDB 5ZJS 5ZJS 1 14 SEQRES 1 A 84 VAL GLY PRO CYS THR PRO ASN PRO GLY LEU HIS GLU TRP SEQRES 2 A 84 THR GLY GLN VAL SER VAL ARG LYS LYS ARG LYS PRO TYR SEQRES 3 A 84 SER LYS PHE GLN THR LEU GLU LEU GLU LYS GLU PHE LEU SEQRES 4 A 84 PHE ASN ALA TYR VAL SER LYS GLN LYS ARG TRP GLU LEU SEQRES 5 A 84 ALA ARG ASN LEU GLN LEU THR GLU ARG GLN VAL LYS ILE SEQRES 6 A 84 TRP PHE GLN ASN ARG ARG MET LYS ASN LYS LYS ASN SER SEQRES 7 A 84 GLN ARG GLN ALA ASN GLN SEQRES 1 B 74 ASP ALA ARG ARG LYS ARG ARG ASN PHE SER LYS GLN ALA SEQRES 2 B 74 SER GLU ILE LEU ASN GLU TYR PHE TYR SER HIS LEU SER SEQRES 3 B 74 ASN PRO TYR PRO SER GLU GLU ALA LYS GLU GLU LEU ALA SEQRES 4 B 74 ARG LYS CYS GLY ILE THR VAL SER GLN VAL SER ASN TRP SEQRES 5 B 74 PHE GLY ASN LYS ARG ILE ARG TYR LYS LYS ASN ILE GLY SEQRES 6 B 74 LYS ALA GLN GLU GLU ALA ASN LEU TYR SEQRES 1 C 14 DG DT DC DA DT DT DA DA DT DC DA DT DG SEQRES 2 C 14 DC SEQRES 1 D 14 DG DC DA DT DG DA DT DT DA DA DT DG DA SEQRES 2 D 14 DC FORMUL 5 HOH *3(H2 O) HELIX 1 AA1 SER A 27 LEU A 39 1 13 HELIX 2 AA2 GLN A 47 LEU A 56 1 10 HELIX 3 AA3 THR A 59 ASN A 77 1 19 HELIX 4 AA4 SER B 10 TYR B 22 1 13 HELIX 5 AA5 GLU B 33 CYS B 42 1 10 HELIX 6 AA6 THR B 45 LYS B 62 1 18 CISPEP 1 ARG B 4 LYS B 5 0 7.66 CISPEP 2 ILE B 64 GLY B 65 0 6.66 CISPEP 3 LYS B 66 ALA B 67 0 -3.17 CRYST1 77.760 49.658 96.774 90.00 109.03 90.00 C 1 2 1 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 0.012860 0.000000 0.004437 0.00000 SCALE2 0.000000 0.020138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010931 0.00000