HEADER IMMUNE SYSTEM 03-JAN-03 1NKO TITLE ENERGETIC AND STRUCTURAL BASIS OF SIALYLATED OLIGOSACCHARIDE TITLE 2 RECOGNITION BY THE NATURAL KILLER CELL INHIBITORY RECEPTOR P75/AIRM1 TITLE 3 OR SIGLEC-7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIALIC ACID BINDING IG-LIKE LECTIN 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL IGV-LIKE DOMAIN RESIDUES 19-150; COMPND 5 SYNONYM: SIGLEC-7, QA79 MEMBRANE PROTEIN, ADHESION INHIBITORY COMPND 6 RECEPTOR MOLECULE-1, AIRM-1, P75, D-SIGLEC; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SIGLEC7 OR AIRM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PT7-7; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P75-1D KEYWDS IMMUNOGLOBULIN, SIGLEC7, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR N.DIMASI,H.ATTRIL,D.M.F.VAN AALTEN,L.MORETTA,R.BIASSONI,R.A.MARIUZZA REVDAT 5 16-AUG-23 1NKO 1 REMARK REVDAT 4 27-OCT-21 1NKO 1 SEQADV REVDAT 3 24-FEB-09 1NKO 1 VERSN REVDAT 2 12-APR-05 1NKO 1 JRNL REVDAT 1 01-APR-03 1NKO 0 JRNL AUTH N.DIMASI,A.MORETTA,L.MORETTA,R.BIASSONI,R.A.MARIUZZA JRNL TITL STRUCTURE OF THE SACCHARIDE-BINDING DOMAIN OF THE HUMAN JRNL TITL 2 NATURAL KILLER CELL INHIBITORY RECEPTOR P75/AIRM1. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 401 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 14747738 JRNL DOI 10.1107/S0907444903028439 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 19760 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.277 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 830 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2525 REMARK 3 BIN R VALUE (WORKING SET) : 0.3780 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 104 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 991 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.01000 REMARK 3 B22 (A**2) : 3.91000 REMARK 3 B33 (A**2) : -0.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 2.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.170 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.830 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.650 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.610 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 54.33 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000017955. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19800 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 15.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 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: AMORE REMARK 200 STARTING MODEL: 1QFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000 20%, NACL 0.2 M, 0.1 M REMARK 280 PHOSPHATE-CITRATE, PH 4.2, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.85750 REMARK 290 SMTRY3 2 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 GLN A 19 REMARK 465 LYS A 20 REMARK 465 GLY A 69 REMARK 465 ASN A 70 REMARK 465 ASP A 71 REMARK 465 ILE A 72 REMARK 465 SER A 73 REMARK 465 HIS A 148 REMARK 465 ARG A 149 REMARK 465 PRO A 150 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 SER A 21 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 67 CD - NE - CZ ANGL. DEV. = 17.2 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 92 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET A 125 CG - SD - CE ANGL. DEV. = 10.2 DEGREES 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 MET A 30 148.35 -172.72 REMARK 500 ASP A 55 59.16 -112.87 REMARK 500 THR A 56 -28.17 -141.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 1NKO A 19 150 UNP Q9Y286 SIGL7_HUMAN 19 150 SEQADV 1NKO ASP A 55 UNP Q9Y286 GLN 55 ENGINEERED MUTATION SEQRES 1 A 132 GLN LYS SER ASN ARG LYS ASP TYR SER LEU THR MET GLN SEQRES 2 A 132 SER SER VAL THR VAL GLN GLU GLY MET CYS VAL HIS VAL SEQRES 3 A 132 ARG CYS SER PHE SER TYR PRO VAL ASP SER ASP THR ASP SEQRES 4 A 132 SER ASP PRO VAL HIS GLY TYR TRP PHE ARG ALA GLY ASN SEQRES 5 A 132 ASP ILE SER TRP LYS ALA PRO VAL ALA THR ASN ASN PRO SEQRES 6 A 132 ALA TRP ALA VAL GLN GLU GLU THR ARG ASP ARG PHE HIS SEQRES 7 A 132 LEU LEU GLY ASP PRO GLN THR LYS ASN CYS THR LEU SER SEQRES 8 A 132 ILE ARG ASP ALA ARG MET SER ASP ALA GLY ARG TYR PHE SEQRES 9 A 132 PHE ARG MET GLU LYS GLY ASN ILE LYS TRP ASN TYR LYS SEQRES 10 A 132 TYR ASP GLN LEU SER VAL ASN VAL THR ALA LEU THR HIS SEQRES 11 A 132 ARG PRO HELIX 1 1 ASN A 22 TYR A 26 5 5 HELIX 2 2 GLN A 88 ARG A 92 5 5 HELIX 3 3 ASP A 100 LYS A 104 5 5 HELIX 4 4 ARG A 114 ALA A 118 5 5 SHEET 1 A 2 SER A 27 MET A 30 0 SHEET 2 A 2 CYS A 46 SER A 49 -1 O SER A 49 N SER A 27 SHEET 1 B 5 SER A 33 GLN A 37 0 SHEET 2 B 5 LEU A 139 THR A 144 1 O SER A 140 N VAL A 34 SHEET 3 B 5 GLY A 119 LYS A 127 -1 N GLY A 119 O VAL A 141 SHEET 4 B 5 HIS A 62 ARG A 67 -1 N HIS A 62 O GLU A 126 SHEET 5 B 5 ALA A 79 THR A 80 -1 O ALA A 79 N TRP A 65 SHEET 1 C 4 SER A 33 GLN A 37 0 SHEET 2 C 4 LEU A 139 THR A 144 1 O SER A 140 N VAL A 34 SHEET 3 C 4 GLY A 119 LYS A 127 -1 N GLY A 119 O VAL A 141 SHEET 4 C 4 ILE A 130 ASN A 133 -1 O ILE A 130 N LYS A 127 SHEET 1 D 3 VAL A 42 VAL A 44 0 SHEET 2 D 3 LEU A 108 ILE A 110 -1 O LEU A 108 N VAL A 44 SHEET 3 D 3 PHE A 95 LEU A 97 -1 N HIS A 96 O SER A 109 SSBOND 1 CYS A 46 CYS A 106 1555 1555 2.00 CRYST1 32.461 49.715 39.787 90.00 113.08 90.00 P 1 21 1 2 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 0.030806 0.000000 0.013129 0.00000 SCALE2 0.000000 0.020115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027321 0.00000