HEADER IMMUNE SYSTEM 16-NOV-18 6ISA TITLE MCD226 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD226 ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PLATELET AND T-CELL ACTIVATION ANTIGEN 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CD226, PTA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IG DOMAIN, NK CELL RECEPTOR, DNAM-1, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,J.QI,S.ZHANG,Y.LI,S.TAN,G.F.GAO REVDAT 3 22-NOV-23 6ISA 1 REMARK REVDAT 2 13-FEB-19 6ISA 1 JRNL REVDAT 1 26-DEC-18 6ISA 0 JRNL AUTH H.WANG,J.QI,S.ZHANG,Y.LI,S.TAN,G.F.GAO JRNL TITL BINDING MODE OF THE SIDE-BY-SIDE TWO-IGV MOLECULE JRNL TITL 2 CD226/DNAM-1 TO ITS LIGAND CD155/NECL-5. JRNL REF PROC. NATL. ACAD. SCI. V. 116 988 2019 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30591568 JRNL DOI 10.1073/PNAS.1815716116 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 15660 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 737 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 40.9584 - 3.4159 0.96 3131 167 0.1799 0.1961 REMARK 3 2 3.4159 - 2.7115 0.99 3066 172 0.2241 0.2471 REMARK 3 3 2.7115 - 2.3688 0.98 3050 140 0.2531 0.2939 REMARK 3 4 2.3688 - 2.1522 0.97 3001 136 0.2418 0.2981 REMARK 3 5 2.1522 - 1.9979 0.87 2675 122 0.2335 0.2846 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 1844 REMARK 3 ANGLE : 0.527 2519 REMARK 3 CHIRALITY : 0.044 284 REMARK 3 PLANARITY : 0.003 318 REMARK 3 DIHEDRAL : 22.276 681 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 6.9386 -2.8791 19.9684 REMARK 3 T TENSOR REMARK 3 T11: 0.1138 T22: 0.1026 REMARK 3 T33: 0.0911 T12: 0.0006 REMARK 3 T13: 0.0016 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 0.8112 L22: 0.4163 REMARK 3 L33: 0.2423 L12: 0.0851 REMARK 3 L13: 0.1689 L23: -0.1105 REMARK 3 S TENSOR REMARK 3 S11: 0.0279 S12: 0.0006 S13: -0.0282 REMARK 3 S21: -0.0220 S22: 0.0042 S23: -0.0244 REMARK 3 S31: 0.0161 S32: -0.0100 S33: 0.0016 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 6ISA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-13 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 : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16031 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 17.1170 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : 0.27000 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: 6ISB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA HEPES (PH 7.5), 10 % (W/V) REMARK 280 PEG 8000, AND 8% (V/V) ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.15950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.23250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.88550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.23250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.15950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.88550 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 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 THR A 1 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 GLN A 27 149.68 -173.22 REMARK 500 SER A 65 129.76 -38.63 REMARK 500 PHE A 69 -6.14 73.59 REMARK 500 SER A 184 58.58 -93.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 438 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 439 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 440 DISTANCE = 6.76 ANGSTROMS DBREF 6ISA A 1 223 UNP Q8K4F0 CD226_MOUSE 21 243 SEQRES 1 A 223 THR LEU TRP ASP THR THR VAL ARG LEU SER GLU THR MET SEQRES 2 A 223 THR LEU GLU CYS VAL TYR PRO LEU THR HIS ASN LEU THR SEQRES 3 A 223 GLN VAL GLU TRP THR LYS ASN THR GLY THR LYS THR VAL SEQRES 4 A 223 SER ILE ALA VAL TYR ASN PRO ASN HIS ASN MET HIS ILE SEQRES 5 A 223 GLU SER ASN TYR LEU HIS ARG VAL HIS PHE LEU ASN SER SEQRES 6 A 223 THR VAL GLY PHE ARG ASN MET SER LEU SER PHE TYR ASN SEQRES 7 A 223 ALA SER GLU ALA ASP ILE GLY ILE TYR SER CYS LEU PHE SEQRES 8 A 223 HIS ALA PHE PRO ASN GLY PRO TRP GLU LYS LYS ILE LYS SEQRES 9 A 223 VAL VAL TRP SER ASP SER PHE GLU ILE ALA ALA PRO SER SEQRES 10 A 223 ASP SER TYR LEU SER ALA GLU PRO GLY GLN ASP VAL THR SEQRES 11 A 223 LEU THR CYS GLN LEU PRO ARG THR TRP PRO VAL GLN GLN SEQRES 12 A 223 VAL ILE TRP GLU LYS VAL GLN PRO HIS GLN VAL ASP ILE SEQRES 13 A 223 LEU ALA SER CYS ASN LEU SER GLN GLU THR ARG TYR THR SEQRES 14 A 223 SER LYS TYR LEU ARG GLN THR ARG SER ASN CYS SER GLN SEQRES 15 A 223 GLY SER MET LYS SER ILE LEU ILE ILE PRO ASN ALA MET SEQRES 16 A 223 ALA ALA ASP SER GLY LEU TYR ARG CYS ARG SER GLU ALA SEQRES 17 A 223 ILE THR GLY LYS ASN LYS SER PHE VAL ILE ARG LEU ILE SEQRES 18 A 223 ILE THR FORMUL 2 HOH *140(H2 O) HELIX 1 AA1 SER A 54 LEU A 57 5 4 HELIX 2 AA2 SER A 80 ILE A 84 5 5 HELIX 3 AA3 MET A 195 SER A 199 5 5 SHEET 1 AA111 MET A 50 ILE A 52 0 SHEET 2 AA111 VAL A 39 TYR A 44 -1 N VAL A 43 O HIS A 51 SHEET 3 AA111 GLN A 27 LYS A 32 -1 N TRP A 30 O ALA A 42 SHEET 4 AA111 GLY A 85 HIS A 92 -1 O HIS A 92 N GLN A 27 SHEET 5 AA111 TRP A 99 VAL A 106 -1 O ILE A 103 N TYR A 87 SHEET 6 AA111 THR A 5 ARG A 8 1 N THR A 5 O LYS A 104 SHEET 7 AA111 GLN A 153 CYS A 160 -1 O VAL A 154 N THR A 6 SHEET 8 AA111 VAL A 141 VAL A 149 -1 N TRP A 146 O LEU A 157 SHEET 9 AA111 GLY A 200 ALA A 208 -1 O ARG A 205 N ILE A 145 SHEET 10 AA111 ASN A 213 ILE A 222 -1 O ILE A 218 N TYR A 202 SHEET 11 AA111 SER A 119 ALA A 123 1 N SER A 119 O ARG A 219 SHEET 1 AA2 3 THR A 14 LEU A 15 0 SHEET 2 AA2 3 LEU A 74 PHE A 76 -1 O LEU A 74 N LEU A 15 SHEET 3 AA2 3 VAL A 60 HIS A 61 -1 N HIS A 61 O SER A 75 SHEET 1 AA3 2 VAL A 129 CYS A 133 0 SHEET 2 AA3 2 SER A 187 ILE A 191 -1 O LEU A 189 N LEU A 131 SSBOND 1 CYS A 17 CYS A 89 1555 1555 2.03 SSBOND 2 CYS A 133 CYS A 204 1555 1555 2.03 SSBOND 3 CYS A 160 CYS A 180 1555 1555 2.03 CISPEP 1 PHE A 94 PRO A 95 0 4.26 CISPEP 2 TRP A 139 PRO A 140 0 7.51 CRYST1 50.319 65.771 70.465 90.00 90.00 90.00 P 21 21 21 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 0.019873 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014191 0.00000