10 20 30 40 50 60 70 80 1T4W - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION 30-APR-04 1T4W
TITLE STRUCTURAL DIFFERENCES IN THE DNA BINDING DOMAINS OF HUMAN TITLE 2 P53 AND ITS C. ELEGANS ORTHOLOG CEP-1: STRUCTURE OF C. TITLE 3 ELEGANS CEP-1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: C.ELEGANS P53 TUMOR SUPPRESSOR-LIKE COMPND 3 TRANSCRIPTION FACTOR; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: DNA BINDING DOMAIN; COMPND 6 SYNONYM: CEP-1; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21
KEYWDS DNA-BINDING DOMAIN, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.HUYEN,P.D.JEFFREY,W.B.DERRY,J.H.ROTHMAN,N.P.PAVLETICH, AUTHOR 2 E.S.STAVRIDI,T.D.HALAZONETIS
REVDAT 2 24-FEB-09 1T4W 1 VERSN REVDAT 1 20-JUL-04 1T4W 0
JRNL AUTH Y.HUYEN,P.D.JEFFREY,W.B.DERRY,J.H.ROTHMAN, JRNL AUTH 2 N.P.PAVLETICH,E.S.STAVRIDI,T.D.HALAZONETIS JRNL TITL STRUCTURAL DIFFERENCES IN THE DNA BINDING DOMAINS JRNL TITL 2 OF HUMAN P53 AND ITS C. ELEGANS ORTHOLOG CEP-1. JRNL REF STRUCTURE V. 12 1237 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15242600 JRNL DOI 10.1016/J.STR.2004.05.007
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1522442.610 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 14247 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1414 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2075 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 241 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1652 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.39000 REMARK 3 B22 (A**2) : -1.37000 REMARK 3 B33 (A**2) : 3.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.79 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 63.39 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1T4W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB022315.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 9.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16384 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, ISOPROPYL ALCOHOL, REMARK 280 DTT, BTP, PH 9.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K
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 19.68000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.09000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.21500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.09000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.68000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.21500 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 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 ALA A 236 -59.02 -23.70 REMARK 500 MET A 346 -160.01 -113.29 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 307 SG REMARK 620 2 HIS A 310 ND1 103.3 REMARK 620 3 CYS A 361 SG 111.5 119.9 REMARK 620 4 CYS A 365 SG 108.1 104.5 108.9 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 201
DBREF 1T4W A 223 418 UNP Q20646 Q20646_CAEEL 223 418
SEQRES 1 A 196 GLU LYS TRP MET GLU ILE ASP VAL LEU LYS GLN LYS VAL SEQRES 2 A 196 ALA LYS SER SER ASP MET ALA PHE ALA ILE SER SER GLU SEQRES 3 A 196 HIS GLU LYS TYR LEU TRP THR LYS MET GLY CYS LEU VAL SEQRES 4 A 196 PRO ILE GLN VAL LYS TRP LYS LEU ASP LYS ARG HIS PHE SEQRES 5 A 196 ASN SER ASN LEU SER LEU ARG ILE ARG PHE VAL LYS TYR SEQRES 6 A 196 ASP LYS LYS GLU ASN VAL GLU TYR ALA ILE ARG ASN PRO SEQRES 7 A 196 ARG SER ASP VAL MET LYS CYS ARG SER HIS THR GLU ARG SEQRES 8 A 196 GLU GLN HIS PHE PRO PHE ASP SER PHE PHE TYR ILE ARG SEQRES 9 A 196 ASN SER GLU HIS GLU PHE SER TYR SER ALA GLU LYS GLY SEQRES 10 A 196 SER THR PHE THR LEU ILE MET TYR PRO GLY ALA VAL GLN SEQRES 11 A 196 ALA ASN PHE ASP ILE ILE PHE MET CYS GLN GLU LYS CYS SEQRES 12 A 196 LEU ASP LEU ASP ASP ARG ARG LYS THR MET CYS LEU ALA SEQRES 13 A 196 VAL PHE LEU ASP ASP GLU ASN GLY ASN GLU ILE LEU HIS SEQRES 14 A 196 ALA TYR ILE LYS GLN VAL ARG ILE VAL ALA TYR PRO ARG SEQRES 15 A 196 ARG ASP TRP LYS ASN PHE CYS GLU ARG GLU ASP ALA LYS SEQRES 16 A 196 GLN
HET ZN A 201 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *155(H2 O)
HELIX 1 1 LEU A 231 ALA A 236 1 6 HELIX 2 2 ASN A 292 ILE A 297 1 6 HELIX 3 3 CYS A 307 ARG A 313 1 7 HELIX 4 4 GLN A 362 LEU A 366 5 5 HELIX 5 5 ASP A 367 ARG A 372 1 6 HELIX 6 6 TYR A 402 LYS A 417 1 16
SHEET 1 A 4 TRP A 225 VAL A 230 0 SHEET 2 A 4 VAL A 261 LYS A 268 -1 O GLN A 264 N ASP A 229 SHEET 3 A 4 GLN A 352 PHE A 359 -1 O ALA A 353 N VAL A 265 SHEET 4 A 4 PHE A 323 ARG A 326 -1 N ARG A 326 O ASP A 356 SHEET 1 B 7 MET A 241 ILE A 245 0 SHEET 2 B 7 LYS A 251 THR A 255 -1 O TYR A 252 N ALA A 244 SHEET 3 B 7 GLU A 388 ILE A 399 1 O GLN A 396 N LEU A 253 SHEET 4 B 7 THR A 374 ASP A 382 -1 N LEU A 381 O ILE A 389 SHEET 5 B 7 SER A 279 TYR A 287 -1 N VAL A 285 O CYS A 376 SHEET 6 B 7 THR A 341 ILE A 345 -1 O LEU A 344 N LEU A 280 SHEET 7 B 7 GLU A 331 SER A 335 -1 N GLU A 331 O ILE A 345
LINK ZN ZN A 201 SG CYS A 307 1555 1555 2.39 LINK ZN ZN A 201 ND1 HIS A 310 1555 1555 1.95 LINK ZN ZN A 201 SG CYS A 361 1555 1555 2.36 LINK ZN ZN A 201 SG CYS A 365 1555 1555 2.40
CISPEP 1 PHE A 317 PRO A 318 0 -0.48
SITE 1 AC1 4 CYS A 307 HIS A 310 CYS A 361 CYS A 365
CRYST1 39.360 68.430 88.180 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 0.025407 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014613 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011340 0.00000