HEADER TRANSCRIPTION ACTIVATOR/DNA 22-NOV-11 3US1 TITLE STRUCTURE OF P63 DNA BINDING DOMAIN IN COMPLEX WITH A 22 BASE PAIR TITLE 2 RESPONSE ELEMENT CONTAINING A TWO BASE PAIR "GC" SPACER BETWEEN HALF TITLE 3 SITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR PROTEIN 63; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: DNA BINDING DOMAIN (UNP RESIDUES 166-362); COMPND 5 SYNONYM: TP63, P63, CHRONIC ULCERATIVE STOMATITIS PROTEIN, CUSP, COMPND 6 KERATINOCYTE TRANSCRIPTION FACTOR KET, TRANSFORMATION-RELATED PROTEIN COMPND 7 63, TUMOR PROTEIN P73-LIKE, P73L, P40, P51; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*GP*CP*AP*AP*AP*CP*AP*TP COMPND 11 *GP*TP*TP*T)-3'; COMPND 12 CHAIN: F; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: P63 RESPONSE ELEMENT WITH GC SPACER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KET, P63, P73H, P73L, TP63, TP73L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS B-DNA DOUBLE HELIX, ZINC BINDING, BETA SANDWICH, GREEK KEY, KEYWDS 2 TRANSCRIPTION FACTOR, NUCLEUS, TRANSCRIPTION ACTIVATOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.CHEN,O.HERZBERG REVDAT 4 13-SEP-23 3US1 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3US1 1 REMARK REVDAT 2 21-MAR-12 3US1 1 JRNL REVDAT 1 01-FEB-12 3US1 0 JRNL AUTH C.CHEN,N.GORLATOVA,O.HERZBERG JRNL TITL PLIABLE DNA CONFORMATION OF RESPONSE ELEMENTS BOUND TO JRNL TITL 2 TRANSCRIPTION FACTOR P63. JRNL REF J.BIOL.CHEM. V. 287 7477 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22247550 JRNL DOI 10.1074/JBC.M111.315820 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 12335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 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 19.6102 - 5.5628 0.99 1450 139 0.1609 0.1916 REMARK 3 2 5.5628 - 4.4321 0.99 1437 125 0.1431 0.1553 REMARK 3 3 4.4321 - 3.8768 0.99 1413 133 0.1622 0.2110 REMARK 3 4 3.8768 - 3.5245 0.99 1400 153 0.2036 0.2371 REMARK 3 5 3.5245 - 3.2732 0.99 1414 120 0.2164 0.2432 REMARK 3 6 3.2732 - 3.0810 0.98 1420 128 0.2526 0.3158 REMARK 3 7 3.0810 - 2.9272 0.97 1350 159 0.3010 0.3084 REMARK 3 8 2.9272 - 2.8000 0.96 1345 149 0.3450 0.3439 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 21.97 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.69630 REMARK 3 B22 (A**2) : 4.29450 REMARK 3 B33 (A**2) : -9.99080 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.03330 REMARK 3 B23 (A**2) : 0.00000 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 : 0.012 3485 REMARK 3 ANGLE : 1.640 4830 REMARK 3 CHIRALITY : 0.108 538 REMARK 3 PLANARITY : 0.010 558 REMARK 3 DIHEDRAL : 21.467 1341 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -47.0960 13.4619 26.5107 REMARK 3 T TENSOR REMARK 3 T11: 0.0472 T22: 0.0443 REMARK 3 T33: 0.0476 T12: 0.0147 REMARK 3 T13: 0.0102 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.2950 L22: 0.4759 REMARK 3 L33: 0.4106 L12: 0.1878 REMARK 3 L13: 0.1495 L23: 0.1618 REMARK 3 S TENSOR REMARK 3 S11: -0.0438 S12: 0.0548 S13: -0.1459 REMARK 3 S21: -0.1510 S22: 0.0185 S23: -0.0221 REMARK 3 S31: 0.0623 S32: 0.0856 S33: -0.0215 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -16.3125 -7.0493 5.0705 REMARK 3 T TENSOR REMARK 3 T11: 0.3068 T22: 0.3457 REMARK 3 T33: 0.2203 T12: -0.0295 REMARK 3 T13: -0.0797 T23: 0.0527 REMARK 3 L TENSOR REMARK 3 L11: 0.6554 L22: 0.4440 REMARK 3 L33: 0.4949 L12: -0.4087 REMARK 3 L13: 0.4123 L23: -0.3572 REMARK 3 S TENSOR REMARK 3 S11: 0.1882 S12: -0.0869 S13: -0.2113 REMARK 3 S21: -0.1141 S22: 0.0184 S23: 0.0644 REMARK 3 S31: 0.2541 S32: -0.2615 S33: 0.0103 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN F REMARK 3 ORIGIN FOR THE GROUP (A): -42.2710 -12.3993 0.2119 REMARK 3 T TENSOR REMARK 3 T11: 0.2764 T22: 0.2764 REMARK 3 T33: 0.1456 T12: 0.0367 REMARK 3 T13: -0.0001 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.4124 L22: 0.1227 REMARK 3 L33: 0.2159 L12: 0.1640 REMARK 3 L13: -0.2993 L23: -0.1418 REMARK 3 S TENSOR REMARK 3 S11: -0.0389 S12: -0.0427 S13: 0.2066 REMARK 3 S21: -0.0717 S22: 0.2372 S23: 0.0666 REMARK 3 S31: 0.4017 S32: 0.1516 S33: 0.4728 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 3US1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000069137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03320357 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12343 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 60.116 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 3QYN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM PHOSPHATE MONOBASIC, REMARK 280 0.1 M BIS-TRIS, PH 6.8, 14% PEG3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K 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 42.47700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.47700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.61000 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, F 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -84.95400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 HOH A 11 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 32 LIES ON A SPECIAL POSITION. REMARK 375 HOH F 129 LIES ON A SPECIAL POSITION. 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 121 REMARK 465 SER A 122 REMARK 465 HIS A 123 REMARK 465 MET A 124 REMARK 465 ALA A 125 REMARK 465 ALA A 148 REMARK 465 ILE A 320 REMARK 465 ARG A 321 REMARK 465 LYS A 322 REMARK 465 GLN A 323 REMARK 465 GLY D 121 REMARK 465 SER D 122 REMARK 465 HIS D 123 REMARK 465 MET D 124 REMARK 465 ALA D 125 REMARK 465 SER D 126 REMARK 465 PRO D 127 REMARK 465 SER D 128 REMARK 465 ASN D 129 REMARK 465 THR D 130 REMARK 465 GLN D 144 REMARK 465 SER D 145 REMARK 465 SER D 146 REMARK 465 THR D 147 REMARK 465 ALA D 148 REMARK 465 LYS D 149 REMARK 465 SER D 150 REMARK 465 ALA D 151 REMARK 465 ARG D 321 REMARK 465 LYS D 322 REMARK 465 GLN D 323 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 SER A 145 OG REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 LYS A 194 CE NZ REMARK 470 ARG A 212 NE CZ NH1 NH2 REMARK 470 GLN A 255 OE1 NE2 REMARK 470 LYS D 160 CG CD CE NZ REMARK 470 LYS D 194 CD CE NZ REMARK 470 ILE D 219 CG1 CG2 CD1 REMARK 470 ARG D 291 CG CD NE CZ NH1 NH2 REMARK 470 ASP D 292 CG OD1 OD2 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 N ASP D 131 O HOH D 61 1.65 REMARK 500 N SER A 126 O HOH A 45 1.86 REMARK 500 O LYS A 168 O HOH A 54 1.97 REMARK 500 O ILE A 305 O HOH A 56 2.12 REMARK 500 OP1 DT F 18 O HOH F 33 2.17 REMARK 500 OH TYR A 192 O HOH A 55 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 300 CB CYS A 300 SG -0.097 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 133 C - N - CA ANGL. DEV. = 9.5 DEGREES 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 PRO A 127 136.80 -20.22 REMARK 500 SER A 146 -149.37 -138.18 REMARK 500 ALA A 151 11.27 -47.70 REMARK 500 ALA A 167 -9.86 61.37 REMARK 500 PRO A 181 -146.21 -37.60 REMARK 500 GLN A 182 -71.79 -94.41 REMARK 500 ALA A 184 130.43 -18.68 REMARK 500 VAL A 198 -38.14 -35.95 REMARK 500 LEU A 210 -43.56 -132.05 REMARK 500 SER A 211 127.50 -29.41 REMARK 500 PHE A 214 -5.59 72.89 REMARK 500 SER A 271 45.76 -86.14 REMARK 500 SER A 272 9.60 -163.54 REMARK 500 ASN A 278 58.80 36.58 REMARK 500 ARG A 279 28.82 49.02 REMARK 500 CYS A 306 -153.80 -134.68 REMARK 500 ALA D 167 6.39 49.48 REMARK 500 PRO D 181 -157.27 -53.56 REMARK 500 ALA D 184 124.93 6.15 REMARK 500 ARG D 212 -52.14 -25.67 REMARK 500 PHE D 214 -15.35 80.44 REMARK 500 GLU D 216 -83.39 -10.06 REMARK 500 ASN D 231 105.21 -165.00 REMARK 500 GLU D 259 26.76 -141.02 REMARK 500 MET D 268 44.46 -107.75 REMARK 500 CYS D 269 143.67 -178.47 REMARK 500 ASN D 278 54.34 37.88 REMARK 500 ARG D 291 -33.61 -38.48 REMARK 500 CYS D 306 -147.55 -131.04 REMARK 500 SER D 319 3.20 -55.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA F 5 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 HIS A 208 ND1 109.0 REMARK 620 3 CYS A 269 SG 111.8 115.3 REMARK 620 4 CYS A 273 SG 108.6 111.7 100.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 205 SG REMARK 620 2 HIS D 208 ND1 102.1 REMARK 620 3 CYS D 269 SG 109.9 115.5 REMARK 620 4 CYS D 273 SG 121.5 110.3 98.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QYM RELATED DB: PDB REMARK 900 STRUCTURE OF P63 DNA BINDING DOMAIN IN COMPLEX WITH A 10 BASE PAIR REMARK 900 A/T RICH RESPONSE ELEMENT HALF SITE REMARK 900 RELATED ID: 3QYN RELATED DB: PDB REMARK 900 STRUCTURE OF P63 DNA BINDING DOMAIN IN COMPLEX WITH A 22 BASE PAIR REMARK 900 A/T RICH RESPONSE ELEMENT CONTAINING 2 BASE PAIR SPACER BETWEEN REMARK 900 HALF SITES REMARK 900 RELATED ID: 3US0 RELATED DB: PDB REMARK 900 STRUCTURE OF P63 DNA BINDING DOMAIN IN COMPLEX WITH A 22 BASE PAIR REMARK 900 A/T RICH RESPONSE ELEMENT CONTAINING A TWO BASE PAIR "AT" SPACER REMARK 900 BETWEEN HALF SITES REMARK 900 RELATED ID: 3US2 RELATED DB: PDB REMARK 900 STRUCTURE OF P63 DNA BINDING DOMAIN IN COMPLEX WITH A 19 BASE PAIR REMARK 900 A/T RICH RESPONSE ELEMENT CONTAINING TWO HALF SITES WITH A SINGLE REMARK 900 BASE PAIR OVERLAP DBREF 3US1 A 127 323 UNP Q9H3D4 P63_HUMAN 166 362 DBREF 3US1 D 127 323 UNP Q9H3D4 P63_HUMAN 166 362 DBREF 3US1 F 1 22 PDB 3US1 3US1 1 22 SEQADV 3US1 GLY A 121 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 SER A 122 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 HIS A 123 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 MET A 124 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 ALA A 125 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 SER A 126 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 GLY D 121 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 SER D 122 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 HIS D 123 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 MET D 124 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 ALA D 125 UNP Q9H3D4 EXPRESSION TAG SEQADV 3US1 SER D 126 UNP Q9H3D4 EXPRESSION TAG SEQRES 1 A 203 GLY SER HIS MET ALA SER PRO SER ASN THR ASP TYR PRO SEQRES 2 A 203 GLY PRO HIS SER PHE ASP VAL SER PHE GLN GLN SER SER SEQRES 3 A 203 THR ALA LYS SER ALA THR TRP THR TYR SER THR GLU LEU SEQRES 4 A 203 LYS LYS LEU TYR CYS GLN ILE ALA LYS THR CYS PRO ILE SEQRES 5 A 203 GLN ILE LYS VAL MET THR PRO PRO PRO GLN GLY ALA VAL SEQRES 6 A 203 ILE ARG ALA MET PRO VAL TYR LYS LYS ALA GLU HIS VAL SEQRES 7 A 203 THR GLU VAL VAL LYS ARG CYS PRO ASN HIS GLU LEU SER SEQRES 8 A 203 ARG GLU PHE ASN GLU GLY GLN ILE ALA PRO PRO SER HIS SEQRES 9 A 203 LEU ILE ARG VAL GLU GLY ASN SER HIS ALA GLN TYR VAL SEQRES 10 A 203 GLU ASP PRO ILE THR GLY ARG GLN SER VAL LEU VAL PRO SEQRES 11 A 203 TYR GLU PRO PRO GLN VAL GLY THR GLU PHE THR THR VAL SEQRES 12 A 203 LEU TYR ASN PHE MET CYS ASN SER SER CYS VAL GLY GLY SEQRES 13 A 203 MET ASN ARG ARG PRO ILE LEU ILE ILE VAL THR LEU GLU SEQRES 14 A 203 THR ARG ASP GLY GLN VAL LEU GLY ARG ARG CYS PHE GLU SEQRES 15 A 203 ALA ARG ILE CYS ALA CYS PRO GLY ARG ASP ARG LYS ALA SEQRES 16 A 203 ASP GLU ASP SER ILE ARG LYS GLN SEQRES 1 D 203 GLY SER HIS MET ALA SER PRO SER ASN THR ASP TYR PRO SEQRES 2 D 203 GLY PRO HIS SER PHE ASP VAL SER PHE GLN GLN SER SER SEQRES 3 D 203 THR ALA LYS SER ALA THR TRP THR TYR SER THR GLU LEU SEQRES 4 D 203 LYS LYS LEU TYR CYS GLN ILE ALA LYS THR CYS PRO ILE SEQRES 5 D 203 GLN ILE LYS VAL MET THR PRO PRO PRO GLN GLY ALA VAL SEQRES 6 D 203 ILE ARG ALA MET PRO VAL TYR LYS LYS ALA GLU HIS VAL SEQRES 7 D 203 THR GLU VAL VAL LYS ARG CYS PRO ASN HIS GLU LEU SER SEQRES 8 D 203 ARG GLU PHE ASN GLU GLY GLN ILE ALA PRO PRO SER HIS SEQRES 9 D 203 LEU ILE ARG VAL GLU GLY ASN SER HIS ALA GLN TYR VAL SEQRES 10 D 203 GLU ASP PRO ILE THR GLY ARG GLN SER VAL LEU VAL PRO SEQRES 11 D 203 TYR GLU PRO PRO GLN VAL GLY THR GLU PHE THR THR VAL SEQRES 12 D 203 LEU TYR ASN PHE MET CYS ASN SER SER CYS VAL GLY GLY SEQRES 13 D 203 MET ASN ARG ARG PRO ILE LEU ILE ILE VAL THR LEU GLU SEQRES 14 D 203 THR ARG ASP GLY GLN VAL LEU GLY ARG ARG CYS PHE GLU SEQRES 15 D 203 ALA ARG ILE CYS ALA CYS PRO GLY ARG ASP ARG LYS ALA SEQRES 16 D 203 ASP GLU ASP SER ILE ARG LYS GLN SEQRES 1 F 22 DA DA DA DC DA DT DG DT DT DT DG DC DA SEQRES 2 F 22 DA DA DC DA DT DG DT DT DT HET ZN A 901 1 HET ZN D 901 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *174(H2 O) HELIX 1 1 CYS A 308 SER A 319 1 12 HELIX 2 2 THR D 157 LEU D 159 5 3 HELIX 3 3 CYS D 205 LEU D 210 1 6 HELIX 4 4 SER D 211 GLU D 216 1 6 HELIX 5 5 CYS D 308 SER D 319 1 12 SHEET 1 A 4 ASP A 139 SER A 141 0 SHEET 2 A 4 THR A 169 LYS A 175 -1 O GLN A 173 N SER A 141 SHEET 3 A 4 THR A 261 PHE A 267 -1 O TYR A 265 N CYS A 170 SHEET 4 A 4 ILE A 226 VAL A 228 -1 N ARG A 227 O ASN A 266 SHEET 1 B 7 TRP A 153 SER A 156 0 SHEET 2 B 7 LYS A 161 GLN A 165 -1 O LYS A 161 N SER A 156 SHEET 3 B 7 VAL A 295 CYS A 306 1 O GLU A 302 N LEU A 162 SHEET 4 B 7 ILE A 282 GLU A 289 -1 N LEU A 288 O LEU A 296 SHEET 5 B 7 VAL A 185 TYR A 192 -1 N ARG A 187 O THR A 287 SHEET 6 B 7 GLN A 245 PRO A 250 -1 O VAL A 249 N ILE A 186 SHEET 7 B 7 GLN A 235 GLU A 238 -1 N VAL A 237 O SER A 246 SHEET 1 C 4 ASP D 139 SER D 141 0 SHEET 2 C 4 THR D 169 LYS D 175 -1 O GLN D 173 N SER D 141 SHEET 3 C 4 THR D 261 PHE D 267 -1 O THR D 261 N ILE D 174 SHEET 4 C 4 ILE D 226 VAL D 228 -1 N ARG D 227 O ASN D 266 SHEET 1 D 7 TRP D 153 SER D 156 0 SHEET 2 D 7 LYS D 161 GLN D 165 -1 O TYR D 163 N THR D 154 SHEET 3 D 7 VAL D 295 CYS D 306 1 O GLU D 302 N LEU D 162 SHEET 4 D 7 ILE D 282 GLU D 289 -1 N LEU D 288 O LEU D 296 SHEET 5 D 7 VAL D 185 TYR D 192 -1 N VAL D 191 O LEU D 283 SHEET 6 D 7 GLN D 245 PRO D 250 -1 O VAL D 249 N ILE D 186 SHEET 7 D 7 GLN D 235 GLU D 238 -1 N VAL D 237 O SER D 246 LINK SG CYS A 205 ZN ZN A 901 1555 1555 2.15 LINK ND1 HIS A 208 ZN ZN A 901 1555 1555 1.99 LINK SG CYS A 269 ZN ZN A 901 1555 1555 2.30 LINK SG CYS A 273 ZN ZN A 901 1555 1555 2.21 LINK SG CYS D 205 ZN ZN D 901 1555 1555 2.20 LINK ND1 HIS D 208 ZN ZN D 901 1555 1555 2.07 LINK SG CYS D 269 ZN ZN D 901 1555 1555 2.33 LINK SG CYS D 273 ZN ZN D 901 1555 1555 2.34 SITE 1 AC1 4 CYS A 205 HIS A 208 CYS A 269 CYS A 273 SITE 1 AC2 4 CYS D 205 HIS D 208 CYS D 269 CYS D 273 CRYST1 84.954 101.220 71.501 90.00 122.78 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 0.011771 0.000000 0.007580 0.00000 SCALE2 0.000000 0.009879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016634 0.00000