HEADER SIGNALING PROTEIN 30-JUL-99 1C8Z TITLE C-TERMINAL DOMAIN OF MOUSE BRAIN TUBBY PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUBBY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 ORGAN: BRAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TUBBY FILLED-BARREL, BETA-BARREL, FILLED-BETA-ROLL, 12-STRANDED-BETA- KEYWDS 2 BARREL, HELIX-FILLED-BARREL, OBESITY BLINDNESS, DEAFNESS, SIGNALING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.J.BOGGON,S.C.MYERS,L.SHAPIRO REVDAT 5 07-FEB-24 1C8Z 1 REMARK SEQADV REVDAT 4 24-FEB-09 1C8Z 1 VERSN REVDAT 3 01-APR-03 1C8Z 1 JRNL REVDAT 2 11-MAY-01 1C8Z 1 HEADER REMARK REVDAT 1 12-DEC-99 1C8Z 0 JRNL AUTH T.J.BOGGON,W.S.SHAN,S.SANTAGATA,S.C.MYERS,L.SHAPIRO JRNL TITL IMPLICATION OF TUBBY PROTEINS AS TRANSCRIPTION FACTORS BY JRNL TITL 2 STRUCTURE-BASED FUNCTIONAL ANALYSIS. JRNL REF SCIENCE V. 286 2119 1999 JRNL REFN ISSN 0036-8075 JRNL PMID 10591637 JRNL DOI 10.1126/SCIENCE.286.5447.2119 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 19244 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 937 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2066 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 509 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.640 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009441. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95370 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14300 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: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% PEG 4000, 0.1M HEPES, 4% 2 REMARK 280 -PROPANOL, 5MM DTT, PH 7.5, VAPOR DIFFUSION, HANGING DROP AT 293K 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 21.76800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.53700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.51150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.53700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.76800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.51150 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 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 272 CG CD CE NZ REMARK 470 LYS A 273 CD CE NZ REMARK 470 MET A 275 CG SD CE REMARK 470 MET A 279 CG SD CE REMARK 470 LYS A 293 CD CE NZ REMARK 470 LYS A 302 NZ REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 LYS A 305 CG CD CE NZ REMARK 470 ARG A 322 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 372 CG CD OE1 OE2 REMARK 470 LYS A 452 CE NZ 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 VAL A 243 92.50 52.07 REMARK 500 ILE A 245 117.07 -9.48 REMARK 500 GLN A 248 -71.74 -110.25 REMARK 500 ASP A 271 -157.98 26.53 REMARK 500 LYS A 273 -72.35 -121.01 REMARK 500 MET A 275 101.80 -54.43 REMARK 500 ASP A 276 -116.93 -140.47 REMARK 500 ARG A 277 54.75 -105.41 REMARK 500 MET A 279 124.19 -8.27 REMARK 500 LYS A 305 -75.31 -58.82 REMARK 500 LYS A 307 -46.89 -139.38 REMARK 500 ARG A 322 -146.37 -123.67 REMARK 500 LEU A 357 -12.81 -49.94 REMARK 500 GLU A 358 -8.29 -59.76 REMARK 500 SER A 359 115.90 95.81 REMARK 500 THR A 361 -16.43 86.64 REMARK 500 VAL A 375 -85.66 -73.76 REMARK 500 LEU A 376 82.26 160.00 REMARK 500 CYS A 399 123.30 -34.83 REMARK 500 CYS A 399 123.01 -33.63 REMARK 500 ASN A 417 89.48 -65.88 REMARK 500 SER A 450 -176.89 -171.07 REMARK 500 ASP A 461 74.43 -155.91 REMARK 500 LEU A 502 -151.42 -71.65 REMARK 500 ALA A 503 71.39 57.90 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 3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 3001 DBREF 1C8Z A 241 505 UNP P50586 TUB_MOUSE 241 505 SEQADV 1C8Z GLY A 241 UNP P50586 PRO 241 CONFLICT SEQADV 1C8Z SER A 242 UNP P50586 PRO 242 CONFLICT SEQADV 1C8Z PHE A 280 UNP P50586 TYR 280 CONFLICT SEQRES 1 A 265 GLY SER VAL ASP ILE GLU VAL GLN ASP LEU GLU GLU PHE SEQRES 2 A 265 ALA LEU ARG PRO ALA PRO GLN GLY ILE THR ILE LYS CYS SEQRES 3 A 265 ARG ILE THR ARG ASP LYS LYS GLY MET ASP ARG GLY MET SEQRES 4 A 265 PHE PRO THR TYR PHE LEU HIS LEU ASP ARG GLU ASP GLY SEQRES 5 A 265 LYS LYS VAL PHE LEU LEU ALA GLY ARG LYS ARG LYS LYS SEQRES 6 A 265 SER LYS THR SER ASN TYR LEU ILE SER VAL ASP PRO THR SEQRES 7 A 265 ASP LEU SER ARG GLY GLY ASP SER TYR ILE GLY LYS LEU SEQRES 8 A 265 ARG SER ASN LEU MET GLY THR LYS PHE THR VAL TYR ASP SEQRES 9 A 265 ASN GLY VAL ASN PRO GLN LYS ALA SER SER SER THR LEU SEQRES 10 A 265 GLU SER GLY THR LEU ARG GLN GLU LEU ALA ALA VAL CYS SEQRES 11 A 265 TYR GLU THR ASN VAL LEU GLY PHE LYS GLY PRO ARG LYS SEQRES 12 A 265 MET SER VAL ILE VAL PRO GLY MET ASN MET VAL HIS GLU SEQRES 13 A 265 ARG VAL CYS ILE ARG PRO ARG ASN GLU HIS GLU THR LEU SEQRES 14 A 265 LEU ALA ARG TRP GLN ASN LYS ASN THR GLU SER ILE ILE SEQRES 15 A 265 GLU LEU GLN ASN LYS THR PRO VAL TRP ASN ASP ASP THR SEQRES 16 A 265 GLN SER TYR VAL LEU ASN PHE HIS GLY ARG VAL THR GLN SEQRES 17 A 265 ALA SER VAL LYS ASN PHE GLN ILE ILE HIS GLY ASN ASP SEQRES 18 A 265 PRO ASP TYR ILE VAL MET GLN PHE GLY ARG VAL ALA GLU SEQRES 19 A 265 ASP VAL PHE THR MET ASP TYR ASN TYR PRO LEU CYS ALA SEQRES 20 A 265 LEU GLN ALA PHE ALA ILE ALA LEU SER SER PHE ASP SER SEQRES 21 A 265 LYS LEU ALA CYS GLU HET PO4 A3000 5 HET PO4 A3001 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 HOH *509(H2 O) HELIX 1 1 ASP A 249 ARG A 256 1 8 HELIX 2 2 ASP A 316 SER A 321 1 6 HELIX 3 3 ASN A 348 ALA A 352 5 5 HELIX 4 4 SER A 355 SER A 359 5 5 HELIX 5 5 THR A 408 ASN A 415 1 8 HELIX 6 6 CYS A 486 SER A 500 1 15 SHEET 1 A13 ILE A 264 ARG A 270 0 SHEET 2 A13 THR A 282 ASP A 288 -1 N PHE A 284 O THR A 269 SHEET 3 A13 ILE A 264 ARG A 270 -1 O LYS A 265 N ASP A 288 SHEET 4 A13 VAL A 476 TYR A 481 -1 O PHE A 477 N ILE A 268 SHEET 5 A13 ASP A 461 ALA A 473 -1 N GLN A 468 O ASP A 480 SHEET 6 A13 ASN A 453 HIS A 458 -1 O PHE A 454 N PHE A 469 SHEET 7 A13 ILE A 421 ASN A 426 -1 O GLN A 425 N ILE A 457 SHEET 8 A13 MET A 384 PRO A 389 -1 O MET A 384 N ASN A 426 SHEET 9 A13 GLU A 365 TYR A 371 -1 O ALA A 368 N ILE A 387 SHEET 10 A13 LYS A 339 TYR A 343 -1 N PHE A 340 O VAL A 369 SHEET 11 A13 GLY A 329 SER A 333 -1 O LYS A 330 N TYR A 343 SHEET 12 A13 SER A 309 SER A 314 -1 O TYR A 311 N LEU A 331 SHEET 13 A13 LYS A 294 LYS A 304 -1 O ALA A 299 N SER A 314 SHEET 1 B 3 VAL A 430 ASN A 432 0 SHEET 2 B 3 SER A 437 PHE A 442 -1 O SER A 437 N ASN A 432 SHEET 3 B 3 ARG A 445 GLN A 448 -1 N ARG A 445 O PHE A 442 CISPEP 1 TYR A 483 PRO A 484 0 0.38 SITE 1 AC1 4 LYS A 452 ALA A 503 HOH A1077 HOH A1276 SITE 1 AC2 2 LEU A 255 ARG A 397 CRYST1 43.536 51.023 121.074 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 0.022969 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008259 0.00000