HEADER CELL ADHESION 23-JUN-22 7Y8H TITLE CRYSTAL STRUCTURE OF SDSCAM FNIII1 DOMAIN, ISOFORM ALPHA7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOWN SYNDROME CELL ADHESION MOLECULES; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHELICERATA; SOURCE 3 ORGANISM_TAXID: 6843; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL SURFACE RECEPTOR, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR Q.CHEN,Y.YU,J.CHENG REVDAT 2 29-NOV-23 7Y8H 1 REMARK REVDAT 1 24-MAY-23 7Y8H 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. 1.80 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 14018 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) : 0.223 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 732 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 38.1900 - 3.0700 0.99 2834 153 0.2010 0.2452 REMARK 3 2 3.0700 - 2.4400 0.99 2832 145 0.2428 0.2872 REMARK 3 3 2.4400 - 2.1300 0.99 2767 170 0.2314 0.2866 REMARK 3 4 2.1300 - 1.9300 0.98 2751 142 0.2341 0.2816 REMARK 3 5 1.9300 - 1.8000 0.76 2102 122 0.2549 0.3153 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) : 0.188 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.943 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.74 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 1524 REMARK 3 ANGLE : 0.759 2085 REMARK 3 CHIRALITY : 0.051 239 REMARK 3 PLANARITY : 0.006 269 REMARK 3 DIHEDRAL : 7.649 1266 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 7Y8H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-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) : 0.97852 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-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14730 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 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: 1VA9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 1,500, 100 MM SPG BUFFER REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 40.98850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.60550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.98850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.60550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 290 REMARK 465 GLY A 321 REMARK 465 ASP A 322 REMARK 465 ASN A 323 REMARK 465 GLU A 337 REMARK 465 SER A 338 REMARK 465 ARG A 339 REMARK 465 SER A 340 REMARK 465 TYR B 318 REMARK 465 GLY B 319 REMARK 465 ASN B 320 REMARK 465 GLY B 321 REMARK 465 ASP B 322 REMARK 465 ASN B 323 REMARK 465 THR B 324 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 HH22 ARG B 298 O HOH B 504 1.57 REMARK 500 O HOH A 520 O HOH A 545 1.99 REMARK 500 O HOH B 506 O HOH B 554 2.00 REMARK 500 O HOH B 503 O HOH B 539 2.01 REMARK 500 O HOH A 523 O HOH A 543 2.03 REMARK 500 O GLN B 348 O HOH B 501 2.14 REMARK 500 OG1 THR A 361 O HOH A 501 2.14 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 HH22 ARG A 331 OD1 ASP A 335 2556 1.34 REMARK 500 NH2 ARG A 331 OD1 ASP A 335 2556 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 THR A 306 -158.81 -122.04 REMARK 500 ASP A 335 68.09 -102.12 REMARK 500 THR A 350 41.16 -86.36 REMARK 500 ASN A 371 -162.98 -128.04 REMARK 500 SER A 379 167.34 -47.96 REMARK 500 THR B 306 -155.47 -111.79 REMARK 500 THR B 350 39.84 -94.32 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7Y8H A 293 389 UNP A0A159W468_MESMA DBREF2 7Y8H A A0A159W468 293 389 DBREF1 7Y8H B 293 389 UNP A0A159W468_MESMA DBREF2 7Y8H B A0A159W468 293 389 SEQADV 7Y8H GLY A 290 UNP A0A159W46 EXPRESSION TAG SEQADV 7Y8H ALA A 291 UNP A0A159W46 EXPRESSION TAG SEQADV 7Y8H SER A 292 UNP A0A159W46 EXPRESSION TAG SEQADV 7Y8H GLY B 290 UNP A0A159W46 EXPRESSION TAG SEQADV 7Y8H ALA B 291 UNP A0A159W46 EXPRESSION TAG SEQADV 7Y8H SER B 292 UNP A0A159W46 EXPRESSION TAG SEQRES 1 A 100 GLY ALA SER PRO PRO SER PRO PRO ARG GLY ILE LYS VAL SEQRES 2 A 100 SER GLU VAL THR THR ARG THR ALA ARG LEU SER TRP GLN SEQRES 3 A 100 SER PRO TYR GLY ASN GLY ASP ASN THR VAL VAL THR TYR SEQRES 4 A 100 ILE VAL ARG TYR TRP ARG ASP GLU GLU SER ARG SER GLN SEQRES 5 A 100 LEU HIS GLN LEU THR PHE GLN VAL THR SER ALA ASN LEU SEQRES 6 A 100 LYS ASP LEU HIS PRO GLY THR SER TYR ALA VAL GLN ILE SEQRES 7 A 100 LEU ALA GLU ASN ASP VAL GLY ALA SER ILE PRO SER ARG SEQRES 8 A 100 LEU VAL GLN PHE ARG THR ILE GLU GLU SEQRES 1 B 100 GLY ALA SER PRO PRO SER PRO PRO ARG GLY ILE LYS VAL SEQRES 2 B 100 SER GLU VAL THR THR ARG THR ALA ARG LEU SER TRP GLN SEQRES 3 B 100 SER PRO TYR GLY ASN GLY ASP ASN THR VAL VAL THR TYR SEQRES 4 B 100 ILE VAL ARG TYR TRP ARG ASP GLU GLU SER ARG SER GLN SEQRES 5 B 100 LEU HIS GLN LEU THR PHE GLN VAL THR SER ALA ASN LEU SEQRES 6 B 100 LYS ASP LEU HIS PRO GLY THR SER TYR ALA VAL GLN ILE SEQRES 7 B 100 LEU ALA GLU ASN ASP VAL GLY ALA SER ILE PRO SER ARG SEQRES 8 B 100 LEU VAL GLN PHE ARG THR ILE GLU GLU HET SO4 A 401 5 HET SO4 B 401 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *106(H2 O) SHEET 1 AA1 3 ARG A 298 VAL A 305 0 SHEET 2 AA1 3 ALA A 310 GLN A 315 -1 O GLN A 315 N ARG A 298 SHEET 3 AA1 3 SER A 351 LEU A 354 -1 O ALA A 352 N LEU A 312 SHEET 1 AA2 4 LEU A 342 PHE A 347 0 SHEET 2 AA2 4 THR A 327 ARG A 334 -1 N VAL A 330 O LEU A 345 SHEET 3 AA2 4 SER A 362 GLU A 370 -1 O GLN A 366 N ARG A 331 SHEET 4 AA2 4 VAL A 382 ARG A 385 -1 O PHE A 384 N TYR A 363 SHEET 1 AA3 3 ARG B 298 SER B 303 0 SHEET 2 AA3 3 ALA B 310 GLN B 315 -1 O SER B 313 N LYS B 301 SHEET 3 AA3 3 SER B 351 LEU B 354 -1 O ALA B 352 N LEU B 312 SHEET 1 AA4 4 HIS B 343 PHE B 347 0 SHEET 2 AA4 4 THR B 327 ARG B 334 -1 N VAL B 330 O LEU B 345 SHEET 3 AA4 4 SER B 362 GLU B 370 -1 O GLU B 370 N THR B 327 SHEET 4 AA4 4 VAL B 382 ARG B 385 -1 O PHE B 384 N TYR B 363 CRYST1 81.977 43.211 48.338 90.00 111.29 90.00 C 1 2 1 8 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 0.012199 0.000000 0.004753 0.00000 SCALE2 0.000000 0.023142 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022202 0.00000