HEADER TRANSCRIPTION 21-MAR-18 6G1L TITLE MITF/CLEARBOX STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CLEAR-BOX; COMPND 7 CHAIN: B; COMPND 8 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 GENE: MITF, BW, MI, VIT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 12 ORGANISM_TAXID: 10090 KEYWDS MELANOCYTE, AUTOPHAGY, TRANSCRIPTION FACTOR, DNA BINDING, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR V.POGENBERG,M.WILMANNS REVDAT 3 17-JAN-24 6G1L 1 REMARK REVDAT 2 13-FEB-19 6G1L 1 JRNL REVDAT 1 06-FEB-19 6G1L 0 JRNL AUTH K.MOLLER,S.SIGURBJORNSDOTTIR,A.O.ARNTHORSSON,V.POGENBERG, JRNL AUTH 2 R.DILSHAT,V.FOCK,S.H.BRYNJOLFSDOTTIR,C.BINDESBOLL, JRNL AUTH 3 M.BESSADOTTIR,H.M.OGMUNDSDOTTIR,A.SIMONSEN,L.LARUE, JRNL AUTH 4 M.WILMANNS,V.THORSSON,E.STEINGRIMSSON,M.H.OGMUNDSDOTTIR JRNL TITL MITF HAS A CENTRAL ROLE IN REGULATING STARVATION-INDUCED JRNL TITL 2 AUTOPHAGY IN MELANOMA. JRNL REF SCI REP V. 9 1055 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 30705290 JRNL DOI 10.1038/S41598-018-37522-6 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 10448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 460 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 40.5909 - 3.4610 0.99 3406 164 0.1901 0.2348 REMARK 3 2 3.4610 - 2.7472 1.00 3305 136 0.2456 0.2672 REMARK 3 3 2.7472 - 2.4000 0.99 3277 160 0.2956 0.3263 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.810 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 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 : 0.008 1034 REMARK 3 ANGLE : 0.856 1454 REMARK 3 CHIRALITY : 0.043 156 REMARK 3 PLANARITY : 0.005 137 REMARK 3 DIHEDRAL : 29.478 433 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 6G1L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009215. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.966 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10459 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 41.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.76300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 4ATI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9 M SODIUM MALONATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 22.04550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.44700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.92900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.44700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.04550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.92900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.04550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.92900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.44700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.92900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.04550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.44700 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 51.92900 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 306 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 176 REMARK 465 ALA A 177 REMARK 465 MET A 178 REMARK 465 ALA A 179 REMARK 465 ASN A 180 REMARK 465 ILE A 181 REMARK 465 LYS A 182 REMARK 465 ARG A 183 REMARK 465 GLU A 184 REMARK 465 LEU A 185 REMARK 465 THR A 186 REMARK 465 ALA A 187 REMARK 465 CYS A 188 REMARK 465 ILE A 189 REMARK 465 PHE A 190 REMARK 465 PRO A 191 REMARK 465 THR A 192 REMARK 465 GLU A 193 REMARK 465 SER A 194 REMARK 465 GLU A 195 REMARK 465 ALA A 196 REMARK 465 ARG A 197 REMARK 465 ALA A 198 REMARK 465 LEU A 199 REMARK 465 ARG A 279 REMARK 465 HIS A 280 REMARK 465 LEU A 281 REMARK 465 LEU A 282 REMARK 465 LEU A 283 REMARK 465 ARG A 284 REMARK 465 VAL A 285 REMARK 465 GLN A 286 REMARK 465 GLU A 287 REMARK 465 LEU A 288 REMARK 465 GLU A 289 REMARK 465 MET A 290 REMARK 465 GLN A 291 REMARK 465 ALA A 292 REMARK 465 ARG A 293 REMARK 465 ALA A 294 REMARK 465 HIS A 295 REMARK 465 GLY A 296 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 201 CG CD CE NZ REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 LYS A 272 CG CD CE NZ DBREF 6G1L A 180 296 UNP Q08874 MITF_MOUSE 180 296 DBREF 6G1L B 1 16 PDB 6G1L 6G1L 1 16 SEQADV 6G1L GLY A 176 UNP Q08874 EXPRESSION TAG SEQADV 6G1L ALA A 177 UNP Q08874 EXPRESSION TAG SEQADV 6G1L MET A 178 UNP Q08874 EXPRESSION TAG SEQADV 6G1L ALA A 179 UNP Q08874 EXPRESSION TAG SEQRES 1 A 121 GLY ALA MET ALA ASN ILE LYS ARG GLU LEU THR ALA CYS SEQRES 2 A 121 ILE PHE PRO THR GLU SER GLU ALA ARG ALA LEU ALA LYS SEQRES 3 A 121 GLU ARG GLN LYS LYS ASP ASN HIS ASN LEU ILE GLU ARG SEQRES 4 A 121 ARG ARG ARG PHE ASN ILE ASN ASP ARG ILE LYS GLU LEU SEQRES 5 A 121 GLY THR LEU ILE PRO LYS SER ASN ASP PRO ASP MET ARG SEQRES 6 A 121 TRP ASN LYS GLY THR ILE LEU LYS ALA SER VAL ASP TYR SEQRES 7 A 121 ILE ARG LYS LEU GLN ARG GLU GLN GLN ARG ALA LYS ASP SEQRES 8 A 121 LEU GLU ASN ARG GLN LYS LYS LEU GLU HIS ALA ASN ARG SEQRES 9 A 121 HIS LEU LEU LEU ARG VAL GLN GLU LEU GLU MET GLN ALA SEQRES 10 A 121 ARG ALA HIS GLY SEQRES 1 B 16 DA DG DT DA DT DC DA DC DG DT DG DA DT SEQRES 2 B 16 DA DC DT FORMUL 3 HOH *17(H2 O) HELIX 1 AA1 ALA A 200 ILE A 231 1 32 HELIX 2 AA2 ASN A 242 ASN A 278 1 37 CRYST1 44.091 103.858 112.894 90.00 90.00 90.00 I 21 21 21 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 0.022680 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008858 0.00000