HEADER TRANSCRIPTION REGULATOR/DNA 15-AUG-16 5SZX TITLE EPSTEIN-BARR VIRUS ZTA DNA BINDING DOMAIN HOMODIMER IN COMPLEX WITH TITLE 2 METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*TP*TP*CP*AP*TP*(5CM) COMPND 3 P*GP*CP*TP*CP*AP*GP*TP*GP*CP*T)-3'); COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*GP*(5CM) COMPND 8 P*GP*AP*TP*GP*AP*AP*G)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ZTA TRANSCRIPTION FACTOR; COMPND 13 CHAIN: A, B; COMPND 14 FRAGMENT: DNA BINDING DOMAIN (UNP RESIDUES 175-236); COMPND 15 SYNONYM: EB1,ZEBRA; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: EPSTEIN-BARR VIRUS; SOURCE 11 ORGANISM_COMMON: HHV-4, HUMAN HERPESVIRUS 4; SOURCE 12 ORGANISM_TAXID: 10376; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZTA, ZEBRA, BZLF-1, AP-1, EPSTEIN-BARR VIRUS, EBV, 5-METHYLCYTOSINE, KEYWDS 2 5MC, DNA METHYLATION, TRANSCRIPTION FACTOR, BASIC LEUCINE-ZIPPER, KEYWDS 3 BZIP, TRANSCRIPTION REGULATOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.HONG,J.R.HORTON,X.CHENG REVDAT 5 04-OCT-23 5SZX 1 REMARK REVDAT 4 04-DEC-19 5SZX 1 REMARK REVDAT 3 27-SEP-17 5SZX 1 REMARK REVDAT 2 03-MAY-17 5SZX 1 JRNL REVDAT 1 01-MAR-17 5SZX 0 JRNL AUTH S.HONG,D.WANG,J.R.HORTON,X.ZHANG,S.H.SPECK,R.M.BLUMENTHAL, JRNL AUTH 2 X.CHENG JRNL TITL METHYL-DEPENDENT AND SPATIAL-SPECIFIC DNA RECOGNITION BY THE JRNL TITL 2 ORTHOLOGOUS TRANSCRIPTION FACTORS HUMAN AP-1 AND JRNL TITL 3 EPSTEIN-BARR VIRUS ZTA. JRNL REF NUCLEIC ACIDS RES. V. 45 2503 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28158710 JRNL DOI 10.1093/NAR/GKX057 REMARK 2 REMARK 2 RESOLUTION. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 10725 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 537 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 32.9624 - 3.5725 0.98 2964 157 0.2209 0.2436 REMARK 3 2 3.5725 - 2.8361 0.97 2823 147 0.3014 0.3296 REMARK 3 3 2.8361 - 2.4778 0.94 2696 142 0.3486 0.3779 REMARK 3 4 2.4778 - 2.2513 0.59 1705 91 0.3612 0.3833 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.640 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 : 0.008 1761 REMARK 3 ANGLE : 0.833 2533 REMARK 3 CHIRALITY : 0.035 286 REMARK 3 PLANARITY : 0.009 200 REMARK 3 DIHEDRAL : 24.903 707 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): 115.0661 -0.1030 -74.5322 REMARK 3 T TENSOR REMARK 3 T11: 0.4740 T22: 0.2989 REMARK 3 T33: 0.3931 T12: -0.0357 REMARK 3 T13: 0.2283 T23: 0.0338 REMARK 3 L TENSOR REMARK 3 L11: 3.1617 L22: 3.1944 REMARK 3 L33: 3.9493 L12: 0.6525 REMARK 3 L13: 1.5104 L23: 1.4667 REMARK 3 S TENSOR REMARK 3 S11: 0.2027 S12: 0.0059 S13: 0.2615 REMARK 3 S21: 0.5625 S22: -0.1381 S23: 0.1295 REMARK 3 S31: 0.2800 S32: -0.4168 S33: -0.1331 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 5SZX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10789 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.88500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.090 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: 2C9L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NAH2PO4-H2O 20% PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 47.77450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.36600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.77450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.36600 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 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 C4 DG D 119 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 303 LIES ON A SPECIAL POSITION. 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 GLU A 176 CG CD OE1 OE2 REMARK 470 ILE A 177 CG1 CG2 CD1 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 GLN A 195 OE1 NE2 REMARK 470 GLN A 198 CD OE1 NE2 REMARK 470 GLU A 210 CG CD OE1 OE2 REMARK 470 ARG A 213 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 LEU A 225 CG CD1 CD2 REMARK 470 ASP A 226 CG OD1 OD2 REMARK 470 VAL A 227 CG1 CG2 REMARK 470 ASP A 228 CG OD1 OD2 REMARK 470 SER A 229 OG REMARK 470 ILE A 230 CG1 CG2 CD1 REMARK 470 ILE A 231 CG1 CG2 CD1 REMARK 470 ARG A 233 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 176 CG CD OE1 OE2 REMARK 470 LYS B 178 CD CE NZ REMARK 470 LYS B 181 CG CD CE NZ REMARK 470 LYS B 188 CD CE NZ REMARK 470 LYS B 207 NZ REMARK 470 ARG B 213 CZ NH1 NH2 REMARK 470 LYS B 219 CE NZ REMARK 470 GLN B 220 CG CD OE1 NE2 REMARK 470 LEU B 225 CG CD1 CD2 REMARK 470 ASP B 226 CG OD1 OD2 REMARK 470 VAL B 227 CG1 CG2 REMARK 470 ASP B 228 CG OD1 OD2 REMARK 470 SER B 229 OG REMARK 470 ILE B 230 CG1 CG2 CD1 REMARK 470 ARG B 233 CG CD NE CZ NH1 NH2 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 ASP A 228 -12.42 68.10 REMARK 500 PRO A 235 -178.01 -65.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5T01 RELATED DB: PDB DBREF 5SZX C 1 18 PDB 5SZX 5SZX 1 18 DBREF 5SZX D 102 119 PDB 5SZX 5SZX 102 119 DBREF 5SZX A 175 236 UNP P03206 BZLF1_EBVB9 175 236 DBREF 5SZX B 175 236 UNP P03206 BZLF1_EBVB9 175 236 SEQADV 5SZX SER A 189 UNP P03206 CYS 189 ENGINEERED MUTATION SEQADV 5SZX SER B 189 UNP P03206 CYS 189 ENGINEERED MUTATION SEQRES 1 C 18 DT DC DT DT DC DA DT 5CM DG DC DT DC DA SEQRES 2 C 18 DG DT DG DC DT SEQRES 1 D 18 DA DA DG DC DA DC DT DG DA DG 5CM DG DA SEQRES 2 D 18 DT DG DA DA DG SEQRES 1 A 62 LEU GLU ILE LYS ARG TYR LYS ASN ARG VAL ALA SER ARG SEQRES 2 A 62 LYS SER ARG ALA LYS PHE LYS GLN LEU LEU GLN HIS TYR SEQRES 3 A 62 ARG GLU VAL ALA ALA ALA LYS SER SER GLU ASN ASP ARG SEQRES 4 A 62 LEU ARG LEU LEU LEU LYS GLN MET CYS PRO SER LEU ASP SEQRES 5 A 62 VAL ASP SER ILE ILE PRO ARG THR PRO ASP SEQRES 1 B 62 LEU GLU ILE LYS ARG TYR LYS ASN ARG VAL ALA SER ARG SEQRES 2 B 62 LYS SER ARG ALA LYS PHE LYS GLN LEU LEU GLN HIS TYR SEQRES 3 B 62 ARG GLU VAL ALA ALA ALA LYS SER SER GLU ASN ASP ARG SEQRES 4 B 62 LEU ARG LEU LEU LEU LYS GLN MET CYS PRO SER LEU ASP SEQRES 5 B 62 VAL ASP SER ILE ILE PRO ARG THR PRO ASP HET 5CM C 8 20 HET 5CM D 112 20 HET PO4 A 301 5 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM PO4 PHOSPHATE ION FORMUL 1 5CM 2(C10 H16 N3 O7 P) FORMUL 5 PO4 O4 P 3- FORMUL 6 HOH *14(H2 O) HELIX 1 AA1 LEU A 175 CYS A 222 1 48 HELIX 2 AA2 GLU B 176 CYS B 222 1 47 HELIX 3 AA3 ASP B 226 ILE B 231 1 6 LINK O3' DT C 7 P 5CM C 8 1555 1555 1.55 LINK O3' 5CM C 8 P DG C 9 1555 1555 1.54 LINK O3' DG D 111 P 5CM D 112 1555 1555 1.60 LINK O3' 5CM D 112 P DG D 113 1555 1555 1.60 CISPEP 1 PRO B 235 ASP B 236 0 7.63 SITE 1 AC1 7 TYR A 180 ARG A 183 ARG A 187 ARG B 190 SITE 2 AC1 7 ALA B 191 LYS B 194 DA D 110 CRYST1 95.549 26.732 99.673 90.00 97.25 90.00 C 1 2 1 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 0.010466 0.000000 0.001331 0.00000 SCALE2 0.000000 0.037408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010114 0.00000