HEADER CELL ADHESION 17-DEC-22 8HS7 TITLE CRYSTAL STRUCTURE OF VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED TITLE 2 PROTEIN SCS2 FROM YEAST COMPND MOL_ID: 1; COMPND 2 MOLECULE: VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN COMPND 3 SCS2; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: MSP DOMAIN; COMPND 6 SYNONYM: VAMP-ASSOCIATED PROTEIN SCS2,CHOLINE SENSITIVITY SUPPRESSOR COMPND 7 PROTEIN 2,VAP HOMOLOG 1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SCS2, YER120W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR T.XU REVDAT 1 17-JAN-24 8HS7 0 JRNL AUTH T.XU JRNL TITL CRYSTAL STRUCTURE OF THE MAJOR SPERM PROTEIN DOMAIN OF SCS2 JRNL TITL 2 FROM SACCHAROMYCES CEREVISIAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4778 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10680 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1058 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 40.9200 - 4.0000 1.00 1277 137 0.2168 0.2145 REMARK 3 2 4.0000 - 3.1800 1.00 1220 134 0.2273 0.2635 REMARK 3 3 3.1700 - 2.7700 1.00 1205 135 0.2736 0.2736 REMARK 3 4 2.7700 - 2.5200 1.00 1194 132 0.2893 0.2992 REMARK 3 5 2.5200 - 2.3400 1.00 1192 128 0.2972 0.3340 REMARK 3 6 2.3400 - 2.2000 1.00 1182 131 0.3050 0.3035 REMARK 3 7 2.2000 - 2.0900 1.00 1172 129 0.2963 0.2891 REMARK 3 8 2.0900 - 2.0000 0.99 1180 132 0.3353 0.3463 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.247 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.949 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.45 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 : 0.003 1019 REMARK 3 ANGLE : 0.628 1384 REMARK 3 CHIRALITY : 0.047 161 REMARK 3 PLANARITY : 0.003 176 REMARK 3 DIHEDRAL : 17.816 381 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 8HS7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033505. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978520 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10680 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.05229 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.64310 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.490 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 (%): 55.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1 MM TRIS-BIS (PH REMARK 280 5.5). 0.1 M EDTA, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 37.58267 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 18.79133 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 18.79133 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 37.58267 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: MONOMERIC 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 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 341 LIES ON A SPECIAL POSITION. DBREF 8HS7 A 1 126 UNP P40075 SCS2_YEAST 1 126 SEQRES 1 A 126 MET SER ALA VAL GLU ILE SER PRO ASP VAL LEU VAL TYR SEQRES 2 A 126 LYS SER PRO LEU THR GLU GLN SER THR GLU TYR ALA SER SEQRES 3 A 126 ILE SER ASN ASN SER ASP GLN THR ILE ALA PHE LYS VAL SEQRES 4 A 126 LYS THR THR ALA PRO LYS PHE TYR CYS VAL ARG PRO ASN SEQRES 5 A 126 ALA ALA VAL VAL ALA PRO GLY GLU THR ILE GLN VAL GLN SEQRES 6 A 126 VAL ILE PHE LEU GLY LEU THR GLU GLU PRO ALA ALA ASP SEQRES 7 A 126 PHE LYS CYS ARG ASP LYS PHE LEU VAL ILE THR LEU PRO SEQRES 8 A 126 SER PRO TYR ASP LEU ASN GLY LYS ALA VAL ALA ASP VAL SEQRES 9 A 126 TRP SER ASP LEU GLU ALA GLU PHE LYS GLN GLN ALA ILE SEQRES 10 A 126 SER LYS LYS ILE LYS VAL LYS TYR LEU HET EDT A 201 20 HETNAM EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL- HETNAM 2 EDT AMINO}-ACETIC ACID FORMUL 2 EDT C10 H16 N2 O8 FORMUL 3 HOH *47(H2 O) HELIX 1 AA1 ALA A 100 LYS A 113 1 14 HELIX 2 AA2 GLN A 114 ALA A 116 5 3 SHEET 1 AA1 4 VAL A 4 SER A 7 0 SHEET 2 AA1 4 SER A 21 ASN A 29 -1 O SER A 26 N SER A 7 SHEET 3 AA1 4 THR A 61 PHE A 68 -1 O VAL A 66 N GLU A 23 SHEET 4 AA1 4 TYR A 47 ARG A 50 -1 N CYS A 48 O ILE A 67 SHEET 1 AA2 5 VAL A 10 LYS A 14 0 SHEET 2 AA2 5 ILE A 117 LEU A 126 1 O LYS A 122 N LEU A 11 SHEET 3 AA2 5 LYS A 84 PRO A 91 -1 N PHE A 85 O ILE A 121 SHEET 4 AA2 5 ILE A 35 THR A 41 -1 N LYS A 38 O ILE A 88 SHEET 5 AA2 5 ALA A 53 VAL A 56 -1 O ALA A 54 N PHE A 37 CISPEP 1 SER A 7 PRO A 8 0 -3.82 CISPEP 2 SER A 15 PRO A 16 0 3.96 CISPEP 3 ARG A 50 PRO A 51 0 -5.54 CRYST1 68.689 68.689 56.374 90.00 90.00 120.00 P 32 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 0.014558 0.008405 0.000000 0.00000 SCALE2 0.000000 0.016811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017739 0.00000