HEADER TRANSCRIPTION 28-AUG-02 1MJS TITLE MH2 DOMAIN OF TRANSCRIPTIONAL FACTOR SMAD3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMAD 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MH2 DOMAIN, RESIDUES 229-425; COMPND 5 SYNONYM: MAD3, HMAD-3, MMAD3, JV15-2, HSMAD3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SMAD3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA SANDWICH, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.Y.QIN,S.S.LAM,J.J.CORREIA,K.LIN REVDAT 2 24-FEB-09 1MJS 1 VERSN REVDAT 1 16-OCT-02 1MJS 0 JRNL AUTH B.Y.QIN,S.S.LAM,J.J.CORREIA,K.LIN JRNL TITL SMAD3 ALLOSTERY LINKS TGF-BETA RECEPTOR KINASE JRNL TITL 2 ACTIVATION TO TRANSCRIPTIONAL CONTROL JRNL REF GENES DEV. V. 16 1950 2002 JRNL REFN ISSN 0890-9369 JRNL PMID 12154125 JRNL DOI 10.1101/GAD.1002002 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 14494 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) : 0.196 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 500 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1852 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1398 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.76000 REMARK 3 B22 (A**2) : 0.76000 REMARK 3 B33 (A**2) : -1.53000 REMARK 3 B12 (A**2) : 1.45000 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) : 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.72 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.650 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.680 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.500 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.940 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 83.87 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MJS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-02. REMARK 100 THE RCSB ID CODE IS RCSB016964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14765 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.340 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 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 (%) : 0.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.530 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: SMAD4 ACTIVE FRAGMENT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.61867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.80933 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 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 TYR A 323 REMARK 465 GLY A 324 REMARK 465 TRP A 325 REMARK 465 HIS A 326 REMARK 465 PRO A 327 REMARK 465 GLY A 380 REMARK 465 ALA A 381 REMARK 465 GLU A 382 REMARK 465 TYR A 383 REMARK 465 ARG A 384 REMARK 465 ARG A 385 REMARK 465 GLN A 386 REMARK 465 ILE A 418 REMARK 465 ARG A 419 REMARK 465 CYS A 420 REMARK 465 SER A 421 REMARK 465 SER A 422 REMARK 465 VAL A 423 REMARK 465 SER A 424 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 LEU A 239 -111.40 64.88 REMARK 500 THR A 260 30.00 -88.65 REMARK 500 VAL A 376 -53.81 65.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 20 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A 21 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 38 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 39 DISTANCE = 7.94 ANGSTROMS REMARK 525 HOH A 95 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH A 116 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 118 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 138 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH A 139 DISTANCE = 5.61 ANGSTROMS REMARK 525 HOH A 156 DISTANCE = 5.65 ANGSTROMS REMARK 525 HOH A 157 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A 163 DISTANCE = 11.00 ANGSTROMS REMARK 525 HOH A 173 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A 194 DISTANCE = 10.13 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MK2 RELATED DB: PDB REMARK 900 SMAD3 SBD COMPLEX DBREF 1MJS A 228 424 UNP P84022 SMAD3_HUMAN 229 425 SEQRES 1 A 197 PRO ALA PHE TRP CYS SER ILE SER TYR TYR GLU LEU ASN SEQRES 2 A 197 GLN ARG VAL GLY GLU THR PHE HIS ALA SER GLN PRO SER SEQRES 3 A 197 MET THR VAL ASP GLY PHE THR ASP PRO SER ASN SER GLU SEQRES 4 A 197 ARG PHE CYS LEU GLY LEU LEU SER ASN VAL ASN ARG ASN SEQRES 5 A 197 ALA ALA VAL GLU LEU THR ARG ARG HIS ILE GLY ARG GLY SEQRES 6 A 197 VAL ARG LEU TYR TYR ILE GLY GLY GLU VAL PHE ALA GLU SEQRES 7 A 197 CYS LEU SER ASP SER ALA ILE PHE VAL GLN SER PRO ASN SEQRES 8 A 197 CYS ASN GLN ARG TYR GLY TRP HIS PRO ALA THR VAL CYS SEQRES 9 A 197 LYS ILE PRO PRO GLY CYS ASN LEU LYS ILE PHE ASN ASN SEQRES 10 A 197 GLN GLU PHE ALA ALA LEU LEU ALA GLN SER VAL ASN GLN SEQRES 11 A 197 GLY PHE GLU ALA VAL TYR GLN LEU THR ARG MET CYS THR SEQRES 12 A 197 ILE ARG MET SER PHE VAL LYS GLY TRP GLY ALA GLU TYR SEQRES 13 A 197 ARG ARG GLN THR VAL THR SER THR PRO CYS TRP ILE GLU SEQRES 14 A 197 LEU HIS LEU ASN GLY PRO LEU GLN TRP LEU ASP LYS VAL SEQRES 15 A 197 LEU THR GLN MET GLY SER PRO SER ILE ARG CYS SER SER SEQRES 16 A 197 VAL SER FORMUL 2 HOH *195(H2 O) HELIX 1 1 ASN A 279 GLY A 290 1 12 HELIX 2 2 SER A 316 GLN A 321 1 6 HELIX 3 3 ASN A 343 GLY A 358 1 16 HELIX 4 4 GLY A 358 GLN A 364 1 7 HELIX 5 5 LEU A 365 MET A 368 5 4 HELIX 6 6 ASN A 400 MET A 413 1 14 SHEET 1 A 6 GLN A 241 ALA A 249 0 SHEET 2 A 6 CYS A 232 GLU A 238 -1 N ILE A 234 O PHE A 247 SHEET 3 A 6 TRP A 394 LEU A 399 -1 O TRP A 394 N TYR A 237 SHEET 4 A 6 THR A 370 PHE A 375 -1 N ILE A 371 O LEU A 397 SHEET 5 A 6 ILE A 312 GLN A 315 -1 N GLN A 315 O ARG A 372 SHEET 6 A 6 CYS A 331 ILE A 333 -1 O CYS A 331 N VAL A 314 SHEET 1 B 5 ARG A 267 CYS A 269 0 SHEET 2 B 5 SER A 253 ASP A 257 1 N THR A 255 O PHE A 268 SHEET 3 B 5 VAL A 293 ILE A 298 -1 O LEU A 295 N MET A 254 SHEET 4 B 5 GLU A 301 CYS A 306 -1 O GLU A 301 N ILE A 298 SHEET 5 B 5 ASN A 338 PHE A 342 -1 O LEU A 339 N ALA A 304 CRYST1 54.325 54.325 59.428 90.00 90.00 120.00 P 32 3 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 0.018408 0.010628 0.000000 0.00000 SCALE2 0.000000 0.021255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016827 0.00000 MASTER 284 0 0 6 11 0 0 6 0 0 0 16 END