HEADER STRUCTURAL PROTEIN 01-DEC-17 6BSB TITLE CRYSTAL STRUCTURE OF THE MUCIN-1 SEA DOMAIN, L1105M MUTANT, SELENIUM- TITLE 2 DERIVATIVE 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 30-OCT-24 6BSB 1 REMARK REVDAT 2 17-JUN-20 6BSB 1 JRNL REVDAT 1 05-DEC-18 6BSB 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2306 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.950 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 11913 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.250 REMARK 3 FREE R VALUE TEST SET COUNT : 626 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 19.1487 - 2.5385 1.00 2986 172 0.1630 0.2026 REMARK 3 2 2.5385 - 2.0156 1.00 2877 136 0.1774 0.2217 REMARK 3 3 2.0156 - 1.7610 1.00 2810 163 0.1852 0.2492 REMARK 3 4 1.7610 - 1.6001 0.93 2614 155 0.2335 0.3028 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.42 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 : 0.010 903 REMARK 3 ANGLE : 0.892 1223 REMARK 3 CHIRALITY : 0.053 133 REMARK 3 PLANARITY : 0.007 161 REMARK 3 DIHEDRAL : 14.079 327 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 6BSB 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_1000230949. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-14 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) : 0.9791 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22032 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.832 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2200 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) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.67 REMARK 200 R MERGE FOR SHELL (I) : 0.49200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.190 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NATIVE CRYSTALS (SEE RELATED ENTRY) REMARK 280 WERE USED AS SEEDS IN A DROP OF 1:1 MIX OF THE SEMET-DERIVATIVE REMARK 280 (9 MG/ML IN 10 MM TRIS-CL, PH 7.4) AND RESERVOIR SOLUTION (0.1 M REMARK 280 SODIUM ACETATE TRIHYDRATE PH 4.6, 1.75 M SODIUM CHLORIDE, 0.2 M REMARK 280 AMMONIUM SULFATE)., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 26.49667 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 52.99333 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 52.99333 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 26.49667 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: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6090 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 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 1.59 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 TYR A1081 62.24 -110.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 6BSB A 1041 1097 UNP P15941 MUC1_HUMAN 1041 1097 DBREF 6BSB B 1098 1152 UNP P15941 MUC1_HUMAN 1098 1152 SEQADV 6BSB MSE B 1105 UNP P15941 LEU 1105 ENGINEERED MUTATION 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 MSE 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 MSE 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 MODRES 6BSB MSE A 1076 MET MODIFIED RESIDUE HET MSE A1076 17 HET MSE B1105 17 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *64(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 LEU A1087 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 LEU A1087 SHEET 3 AA2 4 PHE A1042 ILE A1049 -1 N PHE A1043 O MSE B1105 SHEET 4 AA2 4 ILE B1136 VAL B1144 -1 O SER B1137 N HIS A1048 LINK C GLU A1075 N MSE A1076 1555 1555 1.33 LINK C MSE A1076 N PHE A1077 1555 1555 1.33 LINK C THR B1104 N MSE B1105 1555 1555 1.33 LINK C MSE B1105 N ALA B1106 1555 1555 1.33 CRYST1 43.700 43.700 79.490 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 0.022883 0.013212 0.000000 0.00000 SCALE2 0.000000 0.026423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012580 0.00000