HEADER TRANSCRIPTION 08-MAR-18 6FX5 TITLE MITF DIMERIZATION MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: 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 KEYWDS MELANOCYTES, BHLHZIP, AUTOPHAGY, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR V.POGENBERG,M.MILEWSKI,M.WILMANNS REVDAT 4 17-JAN-24 6FX5 1 REMARK REVDAT 3 22-JAN-20 6FX5 1 JRNL REVDAT 2 11-DEC-19 6FX5 1 JRNL REVDAT 1 20-MAR-19 6FX5 0 JRNL AUTH V.POGENBERG,J.BALLESTEROS-ALVAREZ,R.SCHOBER, JRNL AUTH 2 I.SIGVALDADOTTIR,A.OBARSKA-KOSINSKA,M.MILEWSKI,R.SCHINDL, JRNL AUTH 3 M.H.OGMUNDSDOTTIR,E.STEINGRIMSSON,M.WILMANNS JRNL TITL MECHANISM OF CONDITIONAL PARTNER SELECTIVITY IN MITF/TFE JRNL TITL 2 FAMILY TRANSCRIPTION FACTORS WITH A CONSERVED COILED COIL JRNL TITL 3 STAMMER MOTIF. JRNL REF NUCLEIC ACIDS RES. V. 48 934 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 31777941 JRNL DOI 10.1093/NAR/GKZ1104 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 9762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.080 REMARK 3 FREE R VALUE TEST SET COUNT : 886 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 33.0492 - 3.7238 0.93 1504 158 0.2130 0.2134 REMARK 3 2 3.7238 - 2.9563 0.95 1494 122 0.2149 0.2240 REMARK 3 3 2.9563 - 2.5827 0.96 1467 162 0.2371 0.2635 REMARK 3 4 2.5827 - 2.3467 0.96 1466 158 0.2344 0.2981 REMARK 3 5 2.3467 - 2.1785 0.97 1463 140 0.2402 0.2991 REMARK 3 6 2.1785 - 2.0501 0.98 1482 146 0.2526 0.3226 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.60 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 : 0.017 1202 REMARK 3 ANGLE : 1.385 1614 REMARK 3 CHIRALITY : 0.105 179 REMARK 3 PLANARITY : 0.009 210 REMARK 3 DIHEDRAL : 20.198 475 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 6FX5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-12 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9762 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 33.045 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10800 REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30300 REMARK 200 FOR SHELL : 3.500 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: 4ATH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS GREW IN CONDITIONS BETWEEN REMARK 280 2.0 M AND 2.4 M AMMONIUM SULFATE AND 0.1 AND 0.15 M CADMIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 19.36000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.41500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.36000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.41500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.40000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.36000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.41500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.40000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.36000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.41500 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 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 412 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 214 REMARK 465 ALA A 215 REMARK 465 MET A 216 REMARK 465 ARG A 217 REMARK 465 PHE A 218 REMARK 465 ASN A 219 REMARK 465 HIS A 295 REMARK 465 GLY A 296 REMARK 465 GLY B 214 REMARK 465 ALA B 215 REMARK 465 MET B 216 REMARK 465 ALA B 294 REMARK 465 HIS B 295 REMARK 465 GLY B 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 233 CG CD CE NZ REMARK 470 ASN A 235 CB CG OD1 ND2 REMARK 470 ASP A 236 CG OD1 OD2 REMARK 470 ARG A 240 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 217 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 LYS B 265 CG CD CE NZ REMARK 470 LYS B 272 CD CE NZ REMARK 470 LYS B 273 CD CE NZ REMARK 470 ARG B 293 CD NE CZ NH1 NH2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 301 DBREF 6FX5 A 217 296 UNP Q08874 MITF_MOUSE 217 296 DBREF 6FX5 B 217 296 UNP Q08874 MITF_MOUSE 217 296 SEQADV 6FX5 GLY A 214 UNP Q08874 EXPRESSION TAG SEQADV 6FX5 ALA A 215 UNP Q08874 EXPRESSION TAG SEQADV 6FX5 MET A 216 UNP Q08874 EXPRESSION TAG SEQADV 6FX5 A UNP Q08874 GLN 258 DELETION SEQADV 6FX5 A UNP Q08874 ARG 259 DELETION SEQADV 6FX5 A UNP Q08874 GLU 260 DELETION SEQADV 6FX5 GLY B 214 UNP Q08874 EXPRESSION TAG SEQADV 6FX5 ALA B 215 UNP Q08874 EXPRESSION TAG SEQADV 6FX5 MET B 216 UNP Q08874 EXPRESSION TAG SEQADV 6FX5 B UNP Q08874 GLN 258 DELETION SEQADV 6FX5 B UNP Q08874 ARG 259 DELETION SEQADV 6FX5 B UNP Q08874 GLU 260 DELETION SEQRES 1 A 80 GLY ALA MET ARG PHE ASN ILE ASN ASP ARG ILE LYS GLU SEQRES 2 A 80 LEU GLY THR LEU ILE PRO LYS SER ASN ASP PRO ASP MET SEQRES 3 A 80 ARG TRP ASN LYS GLY THR ILE LEU LYS ALA SER VAL ASP SEQRES 4 A 80 TYR ILE ARG LYS LEU GLN GLN ARG ALA LYS ASP LEU GLU SEQRES 5 A 80 ASN ARG GLN LYS LYS LEU GLU HIS ALA ASN ARG HIS LEU SEQRES 6 A 80 LEU LEU ARG VAL GLN GLU LEU GLU MET GLN ALA ARG ALA SEQRES 7 A 80 HIS GLY SEQRES 1 B 80 GLY ALA MET ARG PHE ASN ILE ASN ASP ARG ILE LYS GLU SEQRES 2 B 80 LEU GLY THR LEU ILE PRO LYS SER ASN ASP PRO ASP MET SEQRES 3 B 80 ARG TRP ASN LYS GLY THR ILE LEU LYS ALA SER VAL ASP SEQRES 4 B 80 TYR ILE ARG LYS LEU GLN GLN ARG ALA LYS ASP LEU GLU SEQRES 5 B 80 ASN ARG GLN LYS LYS LEU GLU HIS ALA ASN ARG HIS LEU SEQRES 6 B 80 LEU LEU ARG VAL GLN GLU LEU GLU MET GLN ALA ARG ALA SEQRES 7 B 80 HIS GLY HET SO4 A 301 5 HET SO4 B 301 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *33(H2 O) HELIX 1 AA1 ILE A 220 ILE A 231 1 12 HELIX 2 AA2 ASN A 242 ALA A 294 1 50 HELIX 3 AA3 PHE B 218 ILE B 231 1 14 HELIX 4 AA4 ASN B 242 ARG B 293 1 49 SITE 1 AC1 3 ARG A 223 ARG A 293 LYS B 233 SITE 1 AC2 6 ARG B 223 GLU B 226 HIS B 280 ARG B 284 SITE 2 AC2 6 HOH B 403 HOH B 405 CRYST1 38.720 92.830 86.800 90.00 90.00 90.00 C 2 2 21 16 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 0.025826 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011521 0.00000