HEADER STRUCTURAL PROTEIN 01-DEC-17 6BSC TITLE CRYSTAL STRUCTURE OF THE MUCIN-1 SEA DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUCIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEA DOMAIN, N-TERMINAL; COMPND 5 SYNONYM: MUC-1,BREAST CARCINOMA-ASSOCIATED ANTIGEN DF3,CANCER ANTIGEN COMPND 6 15-3,CA 15-3,CARCINOMA-ASSOCIATED MUCIN,EPISIALIN,H23AG,KREBS VON DEN COMPND 7 LUNGEN-6,KL-6,PEMT,PEANUT-REACTIVE URINARY MUCIN,PUM,POLYMORPHIC COMPND 8 EPITHELIAL MUCIN,PEM,TUMOR-ASSOCIATED EPITHELIAL MEMBRANE ANTIGEN, COMPND 9 EMA,TUMOR-ASSOCIATED MUCIN; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: MUCIN-1; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: SEA DOMAIN, C-TERMINAL; COMPND 15 SYNONYM: MUC-1,BREAST CARCINOMA-ASSOCIATED ANTIGEN DF3,CANCER ANTIGEN COMPND 16 15-3,CA 15-3,CARCINOMA-ASSOCIATED MUCIN,EPISIALIN,H23AG,KREBS VON DEN COMPND 17 LUNGEN-6,KL-6,PEMT,PEANUT-REACTIVE URINARY MUCIN,PUM,POLYMORPHIC COMPND 18 EPITHELIAL MUCIN,PEM,TUMOR-ASSOCIATED EPITHELIAL MEMBRANE ANTIGEN, COMPND 19 EMA,TUMOR-ASSOCIATED MUCIN; COMPND 20 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: MUC1, PUM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: MUC1, PUM; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SEA DOMAIN AUTOPROTEOLYSIS MUC1, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.E.NOGUERA,J.JAKONCIC,M.R.ERMACORA REVDAT 3 13-MAR-24 6BSC 1 REMARK REVDAT 2 17-JUN-20 6BSC 1 JRNL REVDAT 1 05-DEC-18 6BSC 0 JRNL AUTH M.E.NOGUERA,J.JAKONCIC,M.R.ERMACORA JRNL TITL HIGH-RESOLUTION STRUCTURE OF INTRAMOLECULARLY PROTEOLYZED JRNL TITL 2 HUMAN MUCIN-1 SEA DOMAIN. JRNL REF BIOCHIM BIOPHYS ACTA V.1868 40361 2020 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1878-1454 JRNL PMID 31923589 JRNL DOI 10.1016/J.BBAPAP.2020.140361 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2456 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1179 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 19.3623 - 2.6032 1.00 2905 148 0.1680 0.1778 REMARK 3 2 2.6032 - 2.0670 1.00 2763 162 0.1512 0.1747 REMARK 3 3 2.0670 - 1.8059 1.00 2738 148 0.1371 0.1723 REMARK 3 4 1.8059 - 1.6409 1.00 2738 133 0.1487 0.2036 REMARK 3 5 1.6409 - 1.5233 1.00 2708 132 0.1372 0.1705 REMARK 3 6 1.5233 - 1.4335 1.00 2699 153 0.1448 0.1965 REMARK 3 7 1.4335 - 1.3618 1.00 2688 150 0.1616 0.2171 REMARK 3 8 1.3618 - 1.3025 1.00 2691 153 0.1889 0.2630 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.11 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 : 0.007 891 REMARK 3 ANGLE : 0.825 1212 REMARK 3 CHIRALITY : 0.077 134 REMARK 3 PLANARITY : 0.006 160 REMARK 3 DIHEDRAL : 13.012 327 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 6BSC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1000229795. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : SI (111) CHANNEL CUT REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP WAS A 1:1 MIX OF PROTEIN (10 REMARK 280 MG/ML IN 10 MM TRIS-CL, PH 7.4) AND RESERVOIR SOLUTION (0.1 M REMARK 280 SODIUM ACETATE TRIHYDRATE PH 4.6, 2.0 M SODIUM CHLORIDE), VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 27.43333 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 54.86667 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 54.86667 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 27.43333 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: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 PHE B 1146 REMARK 465 PRO B 1147 REMARK 465 PHE B 1148 REMARK 465 SER B 1149 REMARK 465 ALA B 1150 REMARK 465 GLN B 1151 REMARK 465 SER B 1152 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH TYR A 1066 O HOH A 1101 1.37 REMARK 500 O HOH B 1245 O HOH B 1249 2.07 REMARK 500 O HOH A 1132 O HOH A 1143 2.16 REMARK 500 OH TYR A 1066 O HOH A 1101 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1125 O HOH A 1142 4455 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A1091 150.60 -43.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 6BSC A 1041 1097 UNP P15941 MUC1_HUMAN 1041 1097 DBREF 6BSC B 1098 1152 UNP P15941 MUC1_HUMAN 1098 1152 SEQRES 1 A 57 SER PHE PHE PHE LEU SER PHE HIS ILE SER ASN LEU GLN SEQRES 2 A 57 PHE ASN SER SER LEU GLU ASP PRO SER THR ASP TYR TYR SEQRES 3 A 57 GLN GLU LEU GLN ARG ASP ILE SER GLU MET PHE LEU GLN SEQRES 4 A 57 ILE TYR LYS GLN GLY GLY PHE LEU GLY LEU SER ASN ILE SEQRES 5 A 57 LYS PHE ARG PRO GLY SEQRES 1 B 55 SER VAL VAL VAL GLN LEU THR LEU ALA PHE ARG GLU GLY SEQRES 2 B 55 THR ILE ASN VAL HIS ASP VAL GLU THR GLN PHE ASN GLN SEQRES 3 B 55 TYR LYS THR GLU ALA ALA SER ARG TYR ASN LEU THR ILE SEQRES 4 B 55 SER ASP VAL SER VAL SER ASP VAL PRO PHE PRO PHE SER SEQRES 5 B 55 ALA GLN SER FORMUL 3 HOH *92(H2 O) HELIX 1 AA1 ASN A 1055 ASP A 1060 5 6 HELIX 2 AA2 THR A 1063 TYR A 1081 1 19 HELIX 3 AA3 ASN B 1113 TYR B 1124 1 12 HELIX 4 AA4 TYR B 1124 ASN B 1133 1 10 SHEET 1 AA1 3 PHE A1086 LEU A1089 0 SHEET 2 AA1 3 VAL B1099 PHE B1107 -1 O ALA B1106 N GLY A1088 SHEET 3 AA1 3 LYS A1093 PRO A1096 -1 N ARG A1095 O VAL B1100 SHEET 1 AA2 4 PHE A1086 LEU A1089 0 SHEET 2 AA2 4 VAL B1099 PHE B1107 -1 O ALA B1106 N GLY A1088 SHEET 3 AA2 4 PHE A1042 ILE A1049 -1 N LEU A1045 O LEU B1103 SHEET 4 AA2 4 ILE B1136 VAL B1144 -1 O SER B1137 N HIS A1048 CRYST1 43.880 43.880 82.300 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 0.022789 0.013157 0.000000 0.00000 SCALE2 0.000000 0.026315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012151 0.00000