HEADER CELL CYCLE 01-DEC-09 2WZO TITLE THE STRUCTURE OF THE FYR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFORMING GROWTH FACTOR BETA REGULATOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FYR DOMAIN, RESIDUES 179-324; COMPND 5 SYNONYM: NUCLEAR INTERACTOR OF ARF AND MDM2; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PRSETA KEYWDS NUCLEUS, CELL CYCLE, TUMOR SUPPRESSOR EXPDTA X-RAY DIFFRACTION AUTHOR M.M.GARCIA-ALAI,M.D.ALLEN,A.C.JOERGER,M.BYCROFT REVDAT 4 24-JAN-18 2WZO 1 SOURCE REVDAT 3 20-APR-11 2WZO 1 JRNL REMARK REVDAT 2 09-JUN-10 2WZO 1 JRNL REVDAT 1 05-MAY-10 2WZO 0 JRNL AUTH M.M.GARCIA-ALAI,M.D.ALLEN,A.C.JOERGER,M.BYCROFT JRNL TITL THE STRUCTURE OF THE FYR DOMAIN OF TRANSFORMING GROWTH JRNL TITL 2 FACTOR BETA REGULATOR 1 (TBRG1)(PNA) JRNL REF PROTEIN SCI. V. 19 1432 2010 JRNL REFN ISSN 0961-8368 JRNL PMID 20506279 JRNL DOI 10.1002/PRO.404 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20853 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 23.3275 - 3.8509 0.99 2615 156 0.1635 0.1665 REMARK 3 2 3.8509 - 3.0588 1.00 2678 147 0.1560 0.1699 REMARK 3 3 3.0588 - 2.6728 1.00 2640 140 0.1820 0.1933 REMARK 3 4 2.6728 - 2.4287 1.00 2653 156 0.1855 0.2282 REMARK 3 5 2.4287 - 2.2548 1.00 2615 143 0.1739 0.2106 REMARK 3 6 2.2548 - 2.1219 1.00 2642 154 0.1765 0.2044 REMARK 3 7 2.1219 - 2.0157 1.00 2642 157 0.1796 0.2357 REMARK 3 8 2.0157 - 1.9280 1.00 2643 146 0.1834 0.2323 REMARK 3 9 1.9280 - 1.8538 1.00 2626 146 0.1850 0.1988 REMARK 3 10 1.8538 - 1.7899 1.00 2665 129 0.1795 0.1989 REMARK 3 11 1.7899 - 1.7339 1.00 2684 122 0.1914 0.2503 REMARK 3 12 1.7339 - 1.6844 1.00 2664 136 0.1981 0.2777 REMARK 3 13 1.6844 - 1.6400 1.00 2693 108 0.2029 0.2183 REMARK 3 14 1.6400 - 1.6000 1.00 2648 142 0.2192 0.2318 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 : 0.41 REMARK 3 B_SOL : 51.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08860 REMARK 3 B22 (A**2) : 0.08860 REMARK 3 B33 (A**2) : -0.17710 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 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 1158 REMARK 3 ANGLE : 1.391 1572 REMARK 3 CHIRALITY : 0.091 170 REMARK 3 PLANARITY : 0.008 206 REMARK 3 DIHEDRAL : 16.604 418 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 2WZO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1290041905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20876 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 32.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: STRUCTURE INITALLY SOLVED USING MAD, THE USED FOR SOLVING REMARK 200 NATIVE DATASET REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M POTASSIUM/SODIUM TARTRATE, 100MM REMARK 280 HEPES, PH7.5, AT 17OC. 20% GLYCEROL USED AS A CRYOPROTECTANT. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 30.43233 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 60.86467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.86467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.43233 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.9 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ASP A 254 60.62 -167.91 REMARK 500 ASN A 257 55.74 -104.38 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 A2099 DISTANCE = 6.32 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1325 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1326 DBREF 2WZO A 179 324 UNP Q3YBR2 TBRG1_HUMAN 179 324 SEQRES 1 A 146 GLY ARG PRO VAL PHE PRO ILE GLY LEU GLY GLY LEU THR SEQRES 2 A 146 VAL TYR SER LEU GLY GLU ILE ILE THR ASP ARG PRO GLY SEQRES 3 A 146 PHE HIS ASP GLU SER ALA ILE TYR PRO VAL GLY TYR CYS SEQRES 4 A 146 SER THR ARG ILE TYR ALA SER MET LYS CYS PRO ASP GLN SEQRES 5 A 146 LYS CYS LEU TYR THR CYS GLN ILE LYS ASP GLY GLY VAL SEQRES 6 A 146 GLN PRO GLN PHE GLU ILE VAL PRO GLU ASP ASP PRO GLN SEQRES 7 A 146 ASN ALA ILE VAL SER SER SER ALA ASP ALA CYS HIS ALA SEQRES 8 A 146 GLU LEU LEU ARG THR ILE SER THR THR MET GLY LYS LEU SEQRES 9 A 146 MET PRO ASN LEU LEU PRO ALA GLY ALA ASP PHE PHE GLY SEQRES 10 A 146 PHE SER HIS PRO ALA ILE HIS ASN LEU ILE GLN SER CYS SEQRES 11 A 146 PRO GLY ALA ARG LYS CYS ILE ASN TYR GLN TRP VAL LYS SEQRES 12 A 146 PHE ASP VAL HET GOL A1325 6 HET GOL A1326 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *160(H2 O) HELIX 1 1 ARG A 202 PHE A 205 5 4 HELIX 2 2 ASP A 254 ALA A 258 5 5 HELIX 3 3 SER A 263 GLY A 280 1 18 HELIX 4 4 ALA A 289 GLY A 295 1 7 HELIX 5 5 HIS A 298 GLN A 306 1 9 HELIX 6 6 GLY A 310 CYS A 314 5 5 SHEET 1 AA 6 ILE A 185 LEU A 187 0 SHEET 2 AA 6 LEU A 190 GLU A 197 -1 O LEU A 190 N LEU A 187 SHEET 3 AA 6 VAL A 214 ALA A 223 -1 O VAL A 214 N GLU A 197 SHEET 4 AA 6 LYS A 231 ASP A 240 -1 O CYS A 232 N TYR A 222 SHEET 5 AA 6 PRO A 245 PRO A 251 -1 O GLN A 246 N LYS A 239 SHEET 6 AA 6 ILE A 259 SER A 261 -1 O ILE A 259 N ILE A 249 CISPEP 1 PHE A 183 PRO A 184 0 -0.30 SITE 1 AC1 9 ALA A 269 LEU A 272 ARG A 273 SER A 276 SITE 2 AC1 9 LEU A 282 MET A 283 LEU A 286 HOH A2119 SITE 3 AC1 9 HOH A2157 SITE 1 AC2 9 PHE A 247 SER A 263 ALA A 264 ASP A 265 SITE 2 AC2 9 ALA A 291 PHE A 296 HOH A2158 HOH A2159 SITE 3 AC2 9 HOH A2160 CRYST1 53.867 53.867 91.297 90.00 90.00 120.00 P 31 2 1 6 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 0.018564 0.010718 0.000000 0.00000 SCALE2 0.000000 0.021436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010953 0.00000