HEADER CELL ADHESION 24-JUN-22 7Y9A TITLE CRYSTAL STRUCTURE OF SDSCAM IG1-2 DOMAINS, ISOFORM BETA2V6 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: TRICHOPLUSIA NI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS CELL SURFACE RECEPTOR, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR Q.CHEN,Y.YU,J.CHENG REVDAT 2 06-SEP-23 7Y9A 1 REMARK REVDAT 1 24-MAY-23 7Y9A 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. 2.51 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) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 8285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 418 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 26.8800 - 3.6200 1.00 2712 147 0.2141 0.2367 REMARK 3 2 3.6200 - 2.8700 1.00 2649 143 0.2653 0.3279 REMARK 3 3 2.8700 - 2.5100 0.94 2506 128 0.3073 0.3592 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.939 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.73 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 : 0.006 1627 REMARK 3 ANGLE : 1.081 2227 REMARK 3 CHIRALITY : 0.075 294 REMARK 3 PLANARITY : 0.005 263 REMARK 3 DIHEDRAL : 4.494 974 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 7Y9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-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 : 8315 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.21100 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: 3DMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES REMARK 280 PH7.0, 20 % (W/V) PEG 6,000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 21.24650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.50900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.67630 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.24650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.50900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 39.67630 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: 5760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -1 REMARK 465 SER A 0 REMARK 465 THR A 146 REMARK 465 SER A 147 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 HG1 THR A 23 HG1 THR A 23 2555 1.25 REMARK 500 OE1 GLU A 2 O2 FUL B 4 4555 2.12 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 ASP A 46 93.82 -69.49 REMARK 500 HIS A 49 2.93 59.82 REMARK 500 LYS A 81 -22.63 64.97 REMARK 500 GLU A 82 -26.60 -143.80 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Y9A A -1 194 PDB 7Y9A 7Y9A -1 194 SEQRES 1 A 196 GLY SER GLY GLU LEU ASN VAL SER PRO PHE VAL PHE ARG SEQRES 2 A 196 GLU ASN VAL MET VAL GLY GLU LYS VAL THR ALA THR CYS SEQRES 3 A 196 THR THR VAL THR GLU ASP ALA GLN ILE SER PHE LYS TRP SEQRES 4 A 196 PHE LYS ASN GLY LYS GLN ILE ASN ASP ASN GLU HIS ILE SEQRES 5 A 196 LYS VAL LEU TYR TYR THR ASP PHE SER LEU LEU SER ILE SEQRES 6 A 196 ASN PRO VAL LYS ALA ASP ASP SER GLY ASN TYR THR CYS SEQRES 7 A 196 VAL ILE THR ALA LYS GLU LYS SER SER LYS PHE THR ALA SEQRES 8 A 196 THR LEU THR VAL LYS ALA SER PRO GLU TRP LEU ILE GLN SEQRES 9 A 196 PRO GLU ASN VAL GLU SER VAL MET GLY SER ASN ILE SER SEQRES 10 A 196 LEU GLN CYS SER VAL THR GLY ILE PRO THR PRO THR ILE SEQRES 11 A 196 ASN TRP LYS LYS SER GLU THR SER SER GLY THR ASP PHE SEQRES 12 A 196 LYS SER LEU SER THR SER SER ASN ALA ILE ILE LEU PRO SEQRES 13 A 196 GLY GLY THR LEU ASN LEU LEU ARG ILE ILE LYS SER ASP SEQRES 14 A 196 GLU GLY LEU TYR GLU CYS GLN ALA SER ASN GLY ILE GLY SEQRES 15 A 196 ASN ASP LEU ARG LYS THR VAL THR ILE SER VAL PHE ILE SEQRES 16 A 196 PRO HET NAG B 1 24 HET NAG B 2 26 HET BMA B 3 21 HET FUL B 4 20 HET FUL B 5 20 HET NAG C 1 24 HET NAG C 2 26 HET BMA C 3 21 HET FUL C 4 20 HET FUL C 5 20 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUL BETA-L-FUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUL BETA-L-FUCOSE; 6-DEOXY-BETA-L-GALACTOPYRANOSE; L- HETSYN 2 FUL FUCOSE; FUCOSE; 6-DEOXY-BETA-L-GALACTOSE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 2 FUL 4(C6 H12 O5) FORMUL 4 HOH *15(H2 O) HELIX 1 AA1 LYS A 67 SER A 71 5 5 HELIX 2 AA2 ILE A 164 GLU A 168 5 5 SHEET 1 AA1 3 VAL A 20 CYS A 24 0 SHEET 2 AA1 3 SER A 59 ILE A 63 -1 O ILE A 63 N VAL A 20 SHEET 3 AA1 3 ILE A 50 TYR A 54 -1 N LEU A 53 O LEU A 60 SHEET 1 AA2 4 LYS A 42 GLN A 43 0 SHEET 2 AA2 4 SER A 34 LYS A 39 -1 N LYS A 39 O LYS A 42 SHEET 3 AA2 4 GLY A 72 ALA A 80 -1 O THR A 75 N PHE A 38 SHEET 4 AA2 4 LYS A 83 LEU A 91 -1 O LEU A 91 N GLY A 72 SHEET 1 AA3 2 ALA A 95 ILE A 101 0 SHEET 2 AA3 2 SER A 119 ILE A 123 -1 O ILE A 123 N ALA A 95 SHEET 1 AA4 4 VAL A 106 VAL A 109 0 SHEET 2 AA4 4 LEU A 183 PHE A 192 1 O SER A 190 N VAL A 106 SHEET 3 AA4 4 GLY A 169 SER A 176 -1 N TYR A 171 O VAL A 187 SHEET 4 AA4 4 THR A 127 LYS A 132 -1 N THR A 127 O SER A 176 SHEET 1 AA5 3 ILE A 114 LEU A 116 0 SHEET 2 AA5 3 THR A 157 LEU A 160 -1 O LEU A 160 N ILE A 114 SHEET 3 AA5 3 ALA A 150 LEU A 153 -1 N LEU A 153 O THR A 157 SSBOND 1 CYS A 24 CYS A 76 1555 1555 2.03 SSBOND 2 CYS A 118 CYS A 173 1555 1555 2.04 LINK ND2 ASN A 73 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 113 C1 NAG B 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O3 NAG B 1 C1 FUL B 4 1555 1555 1.44 LINK O6 NAG B 1 C1 FUL B 5 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O3 NAG C 1 C1 FUL C 4 1555 1555 1.44 LINK O6 NAG C 1 C1 FUL C 5 1555 1555 1.43 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 CISPEP 1 ASN A 64 PRO A 65 0 -5.24 CISPEP 2 ILE A 123 PRO A 124 0 0.29 CRYST1 63.256 49.018 82.024 90.00 104.66 90.00 I 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 0.015809 0.000000 0.004136 0.00000 SCALE2 0.000000 0.020401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012602 0.00000