HEADER IMMUNE SYSTEM 08-MAR-99 2DL2 TITLE KILLER IMMUNOGLOBULIN RECEPTOR 2DL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (MHC CLASS I NK CELL RECEPTOR PRECURSOR (P58 COMPND 3 NATURAL KILLER CELL RECEPTOR CLONE CL-43)); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: EXTRACELLULAR HLA-CW3 RECOGNITION DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: NATURAL KILLER; SOURCE 6 CELLULAR_LOCATION: SURFACE; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS KIR, NATURAL KILLER RECEPTOR, INHIBITORY RECEPTOR, 2DL2, KEYWDS 2 IMMUNOGLOBULIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.SUN,G.SNYDER REVDAT 5 23-AUG-23 2DL2 1 REMARK REVDAT 4 24-FEB-09 2DL2 1 VERSN REVDAT 3 29-DEC-99 2DL2 2 HEADER REVDAT 2 05-MAY-99 2DL2 1 JRNL REVDAT 1 30-MAR-99 2DL2 0 JRNL AUTH G.A.SNYDER,A.G.BROOKS,P.D.SUN JRNL TITL CRYSTAL STRUCTURE OF THE HLA-CW3 ALLOTYPE-SPECIFIC KILLER JRNL TITL 2 CELL INHIBITORY RECEPTOR KIR2DL2 JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 3864 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10097129 JRNL DOI 10.1073/PNAS.96.7.3864 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 4997 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) : 0.219 REMARK 3 FREE R VALUE : 0.309 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1526 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.40 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 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000602. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4683 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28000 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: 1NKR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 20.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.75000 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: 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 THR A 84 N - CA - C ANGL. DEV. = 16.3 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 HIS A 5 -80.16 -62.15 REMARK 500 ARG A 6 123.94 -177.51 REMARK 500 PRO A 8 -165.22 -76.75 REMARK 500 SER A 9 -82.10 -84.46 REMARK 500 LEU A 10 71.93 76.22 REMARK 500 GLU A 21 17.62 44.76 REMARK 500 VAL A 24 116.99 -167.11 REMARK 500 PHE A 45 52.82 106.62 REMARK 500 LEU A 51 151.95 -40.23 REMARK 500 HIS A 56 88.66 -54.78 REMARK 500 ASP A 57 13.62 118.46 REMARK 500 VAL A 59 -110.31 -119.63 REMARK 500 SER A 60 84.11 155.94 REMARK 500 ALA A 62 110.80 -172.24 REMARK 500 MET A 69 86.79 -48.60 REMARK 500 GLN A 71 -80.37 -23.07 REMARK 500 ASP A 72 8.02 -59.81 REMARK 500 ARG A 78 111.89 -171.24 REMARK 500 SER A 82 -154.27 -174.61 REMARK 500 THR A 84 179.63 10.44 REMARK 500 HIS A 85 -124.01 45.96 REMARK 500 PRO A 87 114.74 -39.85 REMARK 500 GLN A 89 -5.40 53.36 REMARK 500 LEU A 90 150.57 62.45 REMARK 500 SER A 91 -157.35 -82.81 REMARK 500 PRO A 108 -149.33 -68.76 REMARK 500 GLN A 113 114.47 -36.68 REMARK 500 PRO A 114 -83.55 -50.13 REMARK 500 ARG A 141 134.28 53.03 REMARK 500 GLU A 142 51.28 -153.00 REMARK 500 GLU A 144 74.95 144.78 REMARK 500 ALA A 145 -167.93 -116.20 REMARK 500 HIS A 146 -113.17 -133.70 REMARK 500 CYS A 148 63.21 -117.18 REMARK 500 ARG A 149 92.78 -66.38 REMARK 500 PRO A 154 -174.75 -52.02 REMARK 500 LYS A 155 29.08 -64.52 REMARK 500 VAL A 156 88.73 -38.78 REMARK 500 ASN A 157 62.42 35.99 REMARK 500 THR A 159 -171.16 -52.85 REMARK 500 PHE A 160 104.48 -160.40 REMARK 500 ASP A 183 -7.17 -53.51 REMARK 500 SER A 189 -156.83 -90.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 2DL2 A 4 200 UNP P43627 KI2L2_HUMAN 25 221 SEQRES 1 A 197 ALA HIS ARG LYS PRO SER LEU LEU ALA HIS PRO GLY ARG SEQRES 2 A 197 LEU VAL LYS SER GLU GLU THR VAL ILE LEU GLN CYS TRP SEQRES 3 A 197 SER ASP VAL ARG PHE GLU HIS PHE LEU LEU HIS ARG GLU SEQRES 4 A 197 GLY LYS PHE LYS ASP THR LEU HIS LEU ILE GLY GLU HIS SEQRES 5 A 197 HIS ASP GLY VAL SER LYS ALA ASN PHE SER ILE GLY PRO SEQRES 6 A 197 MET MET GLN ASP LEU ALA GLY THR TYR ARG CYS TYR GLY SEQRES 7 A 197 SER VAL THR HIS SER PRO TYR GLN LEU SER ALA PRO SER SEQRES 8 A 197 ASP PRO LEU ASP ILE VAL ILE THR GLY LEU TYR GLU LYS SEQRES 9 A 197 PRO SER LEU SER ALA GLN PRO GLY PRO THR VAL LEU ALA SEQRES 10 A 197 GLY GLU SER VAL THR LEU SER CYS SER SER ARG SER SER SEQRES 11 A 197 TYR ASP MET TYR HIS LEU SER ARG GLU GLY GLU ALA HIS SEQRES 12 A 197 GLU CYS ARG PHE SER ALA GLY PRO LYS VAL ASN GLY THR SEQRES 13 A 197 PHE GLN ALA ASP PHE PRO LEU GLY PRO ALA THR HIS GLY SEQRES 14 A 197 GLY THR TYR ARG CYS PHE GLY SER PHE ARG ASP SER PRO SEQRES 15 A 197 TYR GLU TRP SER ASN SER SER ASP PRO LEU LEU VAL SER SEQRES 16 A 197 VAL ILE FORMUL 2 HOH *29(H2 O) HELIX 1 1 GLN A 71 LEU A 73 5 3 SHEET 1 A 3 LEU A 11 HIS A 13 0 SHEET 2 A 3 VAL A 24 GLN A 27 -1 N GLN A 27 O LEU A 11 SHEET 3 A 3 ASN A 63 ILE A 66 -1 N ILE A 66 O VAL A 24 SHEET 1 B 2 HIS A 36 LEU A 38 0 SHEET 2 B 2 TYR A 80 SER A 82 -1 N SER A 82 O HIS A 36 SHEET 1 C 2 GLY A 75 TYR A 77 0 SHEET 2 C 2 LEU A 97 ILE A 99 -1 N ILE A 99 O GLY A 75 SHEET 1 D 2 THR A 117 LEU A 119 0 SHEET 2 D 2 SER A 198 ILE A 200 1 N SER A 198 O VAL A 118 SHEET 1 E 2 GLY A 173 TYR A 175 0 SHEET 2 E 2 LEU A 195 VAL A 197 -1 N VAL A 197 O GLY A 173 SSBOND 1 CYS A 28 CYS A 79 1555 1555 2.03 SSBOND 2 CYS A 128 CYS A 177 1555 1555 2.03 CISPEP 1 HIS A 13 PRO A 14 0 0.29 CISPEP 2 GLN A 113 PRO A 114 0 0.75 CRYST1 40.500 71.500 88.800 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 0.024691 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011261 0.00000