HEADER CELL ADHESION 16-JUN-22 7Y54 TITLE CRYSTAL STRUCTURE OF SDSCAM IG1 DOMAIN, ISOFORM ALPHA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOWN SYNDROME CELL ADHESION MOLECULES; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHELICERATA; SOURCE 3 ORGANISM_TAXID: 6843; SOURCE 4 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CELL SURFACE RECEPTOR, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR Q.CHEN,Y.YU,J.CHENG REVDAT 2 29-NOV-23 7Y54 1 REMARK REVDAT 1 24-MAY-23 7Y54 0 JRNL AUTH J.CHENG,Y.YU,X.WANG,X.ZHENG,T.LIU,D.HU,Y.JIN,Y.LAI,T.M.FU, JRNL AUTH 2 Q.CHEN JRNL TITL STRUCTURAL BASIS FOR THE SELF-RECOGNITION OF SDSCAM IN JRNL TITL 2 CHELICERATA. JRNL REF NAT COMMUN V. 14 2522 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37130844 JRNL DOI 10.1038/S41467-023-38205-1 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 10339 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 521 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 20.6860 - 2.8352 0.98 2545 153 0.1741 0.2201 REMARK 3 2 2.8352 - 2.2513 0.99 2527 132 0.1874 0.2221 REMARK 3 3 2.2513 - 1.9670 0.98 2464 132 0.1818 0.2380 REMARK 3 4 1.9670 - 1.7872 0.90 2282 104 0.1904 0.2465 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.46 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID -1:14) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6602 -19.4535 5.7503 REMARK 3 T TENSOR REMARK 3 T11: 0.1623 T22: 0.0902 REMARK 3 T33: 0.1104 T12: -0.0189 REMARK 3 T13: -0.0009 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 3.0613 L22: 1.6653 REMARK 3 L33: 1.7327 L12: -0.8837 REMARK 3 L13: -0.3976 L23: 0.3549 REMARK 3 S TENSOR REMARK 3 S11: -0.1526 S12: 0.0065 S13: -0.4545 REMARK 3 S21: 0.0674 S22: 0.1017 S23: 0.0882 REMARK 3 S31: 0.2329 S32: -0.0666 S33: 0.1038 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 15:19) REMARK 3 ORIGIN FOR THE GROUP (A): 15.541 -15.107 -0.374 REMARK 3 T TENSOR REMARK 3 T11: 0.1724 T22: 0.1698 REMARK 3 T33: 0.1674 T12: 0.0714 REMARK 3 T13: 0.0207 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 2.0403 L22: 3.6515 REMARK 3 L33: 1.9304 L12: 1.1145 REMARK 3 L13: -0.4657 L23: -1.3707 REMARK 3 S TENSOR REMARK 3 S11: 0.1043 S12: 0.4150 S13: -0.1491 REMARK 3 S21: -0.3833 S22: 0.0030 S23: -0.2879 REMARK 3 S31: -0.0973 S32: -0.0940 S33: 0.0561 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 20:45) REMARK 3 ORIGIN FOR THE GROUP (A): 0.054 -11.695 9.511 REMARK 3 T TENSOR REMARK 3 T11: 0.1496 T22: 0.1484 REMARK 3 T33: 0.1207 T12: 0.0193 REMARK 3 T13: 0.0056 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.0518 L22: 0.8412 REMARK 3 L33: 1.1351 L12: -0.5454 REMARK 3 L13: -0.2749 L23: -0.2236 REMARK 3 S TENSOR REMARK 3 S11: -0.0416 S12: -0.2308 S13: 0.0714 REMARK 3 S21: 0.1114 S22: 0.0979 S23: 0.0078 REMARK 3 S31: 0.0156 S32: 0.0375 S33: -0.0476 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 46:49) REMARK 3 ORIGIN FOR THE GROUP (A): 15.139 -7.851 9.154 REMARK 3 T TENSOR REMARK 3 T11: 0.3740 T22: 0.4323 REMARK 3 T33: 0.4695 T12: -0.0143 REMARK 3 T13: -0.0713 T23: -0.1093 REMARK 3 L TENSOR REMARK 3 L11: 3.4764 L22: 2.8183 REMARK 3 L33: 2.8414 L12: -2.6175 REMARK 3 L13: 0.6550 L23: 0.1374 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: -0.0007 S13: 0.4241 REMARK 3 S21: 0.2339 S22: -0.2600 S23: 0.7981 REMARK 3 S31: -0.5506 S32: 0.0094 S33: -0.0024 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 50:73) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5718 -10.0392 6.2517 REMARK 3 T TENSOR REMARK 3 T11: 0.1154 T22: 0.1102 REMARK 3 T33: 0.1474 T12: 0.0157 REMARK 3 T13: -0.0047 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.8055 L22: 0.3576 REMARK 3 L33: 0.5285 L12: -0.4050 REMARK 3 L13: -0.0729 L23: 0.1022 REMARK 3 S TENSOR REMARK 3 S11: -0.0092 S12: -0.1287 S13: 0.1874 REMARK 3 S21: -0.0020 S22: 0.0343 S23: -0.1439 REMARK 3 S31: 0.0304 S32: 0.0991 S33: -0.0306 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 74:81) REMARK 3 ORIGIN FOR THE GROUP (A): -7.707 -11.446 15.025 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: 0.1882 REMARK 3 T33: 0.0707 T12: 0.0300 REMARK 3 T13: -0.0184 T23: 0.0225 REMARK 3 L TENSOR REMARK 3 L11: 8.0820 L22: 1.1962 REMARK 3 L33: 0.6700 L12: -2.7194 REMARK 3 L13: -1.9281 L23: 0.6543 REMARK 3 S TENSOR REMARK 3 S11: 0.0457 S12: -0.2667 S13: 0.0965 REMARK 3 S21: 0.0616 S22: 0.0447 S23: -0.0805 REMARK 3 S31: 0.0366 S32: -0.0698 S33: -0.0804 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 82:92) REMARK 3 ORIGIN FOR THE GROUP (A): 2.996 -19.933 10.827 REMARK 3 T TENSOR REMARK 3 T11: 0.1396 T22: 0.1874 REMARK 3 T33: 0.1190 T12: 0.0343 REMARK 3 T13: 0.0250 T23: 0.0533 REMARK 3 L TENSOR REMARK 3 L11: 3.2387 L22: 1.3151 REMARK 3 L33: 0.9783 L12: -1.0187 REMARK 3 L13: -0.0514 L23: 0.4088 REMARK 3 S TENSOR REMARK 3 S11: -0.0303 S12: -0.1943 S13: 0.1041 REMARK 3 S21: 0.1801 S22: 0.1163 S23: -0.0680 REMARK 3 S31: 0.1488 S32: -0.1231 S33: -0.0830 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 93:98) REMARK 3 ORIGIN FOR THE GROUP (A): 23.988 -21.902 1.090 REMARK 3 T TENSOR REMARK 3 T11: 0.1721 T22: 0.1473 REMARK 3 T33: 0.1849 T12: 0.0202 REMARK 3 T13: 0.0059 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 5.6021 L22: 2.3790 REMARK 3 L33: 6.0289 L12: -2.0758 REMARK 3 L13: -2.7718 L23: 0.4343 REMARK 3 S TENSOR REMARK 3 S11: -0.3448 S12: 0.4276 S13: 0.1495 REMARK 3 S21: 0.0871 S22: 0.2503 S23: -0.2139 REMARK 3 S31: 0.3109 S32: 0.0605 S33: 0.0755 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 7Y54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-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) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10665 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.787 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6ZR7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% ISOPROPANOL, 100 MM IMIDAZOLE PH REMARK 280 6.5, 15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 33.69750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.36400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.69750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.36400 REMARK 290 SMTRY3 4 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: 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 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 O GLU A 44 O HOH A 101 2.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Y54 A -1 98 PDB 7Y54 7Y54 -1 98 SEQRES 1 A 100 GLY SER PRO PRO GLU ILE LYS PRO PHE TYR PHE SER SER SEQRES 2 A 100 SER VAL GLN GLU GLY GLN ARG GLU GLN VAL ILE CYS SER SEQRES 3 A 100 ALA ILE THR GLY ASP LEU PRO LEU LEU PHE SER TRP LYS SEQRES 4 A 100 LYS ASP GLY LEU ILE VAL GLU ASN PHE LYS ASP ILE THR SEQRES 5 A 100 LEU VAL THR ASN ASP LEU PHE SER VAL LEU VAL ILE SER SEQRES 6 A 100 SER ILE LYS PRO GLU HIS ILE GLY ASN TYR THR CYS ASN SEQRES 7 A 100 LEU GLU ASN PRO PHE GLY SER ASP VAL HIS THR ALA ALA SEQRES 8 A 100 LEU THR MET LYS VAL PRO GLU LEU SER FORMUL 2 HOH *81(H2 O) HELIX 1 AA1 GLU A 44 PHE A 46 5 3 HELIX 2 AA2 LYS A 66 ILE A 70 5 5 SHEET 1 AA1 4 GLU A 3 LYS A 5 0 SHEET 2 AA1 4 GLU A 19 THR A 27 -1 O SER A 24 N LYS A 5 SHEET 3 AA1 4 SER A 58 ILE A 62 -1 O SER A 58 N CYS A 23 SHEET 4 AA1 4 ILE A 49 THR A 53 -1 N VAL A 52 O VAL A 59 SHEET 1 AA2 2 VAL A 13 GLN A 14 0 SHEET 2 AA2 2 MET A 92 VAL A 94 1 O LYS A 93 N VAL A 13 SHEET 1 AA3 4 LEU A 41 ILE A 42 0 SHEET 2 AA3 4 LEU A 33 LYS A 38 -1 N LYS A 38 O LEU A 41 SHEET 3 AA3 4 GLY A 71 ASN A 79 -1 O ASN A 76 N SER A 35 SHEET 4 AA3 4 GLY A 82 LEU A 90 -1 O ALA A 88 N TYR A 73 SSBOND 1 CYS A 23 CYS A 75 1555 1555 2.05 CISPEP 1 LEU A 30 PRO A 31 0 1.32 CRYST1 67.395 40.728 41.482 90.00 94.18 90.00 C 1 2 1 4 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 0.014838 0.000000 0.001085 0.00000 SCALE2 0.000000 0.024553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024171 0.00000