PDB Short entry for 3H8N HEADER IMMUNE SYSTEM 29-APR-09 3H8N TITLE CRYSTAL STRUCTURE ANALYSIS OF KIR2DS4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: KILLER CELL IMMUNOGLOBULIN-LIKE RECEPTOR 2DS4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MHC CLASS I NK CELL RECEPTOR, NATURAL KILLER-ASSOCIATED COMPND 5 TRANSCRIPT 8, NKAT-8, P58 NATURAL KILLER CELL RECEPTOR CLONE CL-39, COMPND 6 P58 NK RECEPTOR, CL-17, CD158 ANTIGEN-LIKE FAMILY MEMBER I; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD158I, KIR2DS4, KIR2DS4*0010101, KKA3, NKAT8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28C KEYWDS LIGAND-BINDING DOMAINS, CELL MEMBRANE, DISULFIDE BOND, GLYCOPROTEIN, KEYWDS 2 IMMUNOGLOBULIN DOMAIN, MEMBRANE, POLYMORPHISM, RECEPTOR, KEYWDS 3 TRANSMEMBRANE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.GRAEF,D.A.BUSHNELL,P.PARHAM REVDAT 4 06-SEP-23 3H8N 1 REMARK REVDAT 3 01-NOV-17 3H8N 1 REMARK REVDAT 2 10-NOV-09 3H8N 1 JRNL REVDAT 1 20-OCT-09 3H8N 0 JRNL AUTH T.GRAEF,A.K.MOESTA,P.J.NORMAN,L.ABI-RACHED,L.VAGO, JRNL AUTH 2 A.M.OLDER AGUILAR,M.GLEIMER,J.A.HAMMOND,L.A.GUETHLEIN, JRNL AUTH 3 D.A.BUSHNELL,P.J.ROBINSON,P.PARHAM JRNL TITL KIR2DS4 IS A PRODUCT OF GENE CONVERSION WITH KIR3DL2 THAT JRNL TITL 2 INTRODUCED SPECIFICITY FOR HLA-A*11 WHILE DIMINISHING JRNL TITL 3 AVIDITY FOR HLA-C. JRNL REF J.EXP.MED. V. 206 2557 2009 JRNL REFN ISSN 0022-1007 JRNL PMID 19858347 JRNL DOI 10.1084/JEM.20091010 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7778 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 357 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 40.4600 - 3.6010 0.57 2569 124 0.2120 0.2270 REMARK 3 2 3.6010 - 2.8590 0.54 2441 114 0.2500 0.3460 REMARK 3 3 2.8590 - 2.5000 0.53 2411 119 0.3040 0.4020 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 : 0.36 REMARK 3 B_SOL : 50.13 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.74400 REMARK 3 B22 (A**2) : 7.79100 REMARK 3 B33 (A**2) : -11.53500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.010 1562 REMARK 3 ANGLE : 1.358 2122 REMARK 3 CHIRALITY : 0.093 225 REMARK 3 PLANARITY : 0.013 279 REMARK 3 DIHEDRAL : 19.234 559 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 3H8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7795 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 64.4000 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) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.700 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: 1IM9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.22 M MG-FORMATE, 100 MM BIS-TRIS, PH REMARK 280 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K, PH 8.5 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 25.61600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.96700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.42550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.96700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.61600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.42550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 O PHE A 34 O SER A 82 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 87 C - N - CD 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 GLU A 35 -8.37 74.37 REMARK 500 PHE A 45 57.47 30.85 REMARK 500 ILE A 52 46.75 -91.36 REMARK 500 PRO A 71 -18.25 -47.56 REMARK 500 SER A 86 125.66 -34.93 REMARK 500 TYR A 88 179.25 78.66 REMARK 500 PRO A 93 -179.32 -69.43 REMARK 500 ALA A 120 140.75 -39.31 REMARK 500 SER A 133 47.30 -92.69 REMARK 500 THR A 170 -74.97 -109.51 REMARK 500 SER A 189 -175.53 -65.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 56 ASP A 57 -127.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EFX RELATED DB: PDB REMARK 900 STRUCTURE OF A COMPLEX BETWEEN THE HUMAN NATURAL KILLER CELL REMARK 900 RECEPTOR KIR2DL2 AND A CLASS I MHC LIGAND HLA-CW3 REMARK 900 RELATED ID: 1IM9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN NATURAL KILLER CELL INHIBITORY REMARK 900 RECEPTOR KIR2DL1 BOUND TO ITS MHC LIGAND HLA-CW4 DBREF 3H8N A 6 200 UNP P43632 KI2S4_HUMAN 27 221 SEQRES 1 A 195 ARG LYS PRO SER PHE LEU ALA LEU PRO GLY HIS LEU VAL SEQRES 2 A 195 LYS SER GLU GLU THR VAL ILE LEU GLN CYS TRP SER ASP SEQRES 3 A 195 VAL MET PHE GLU HIS PHE LEU LEU HIS ARG GLU GLY LYS SEQRES 4 A 195 PHE ASN ASN THR LEU HIS LEU ILE GLY GLU HIS HIS ASP SEQRES 5 A 195 GLY VAL SER LYS ALA ASN PHE SER ILE GLY PRO MET MET SEQRES 6 A 195 PRO VAL LEU ALA GLY THR TYR ARG CYS TYR GLY SER VAL SEQRES 7 A 195 PRO HIS SER PRO TYR GLN LEU SER ALA PRO SER ASP PRO SEQRES 8 A 195 LEU ASP MET VAL ILE ILE GLY LEU TYR GLU LYS PRO SER SEQRES 9 A 195 LEU SER ALA GLN PRO GLY PRO THR VAL GLN ALA GLY GLU SEQRES 10 A 195 ASN VAL THR LEU SER CYS SER SER ARG SER SER TYR ASP SEQRES 11 A 195 MET TYR HIS LEU SER ARG GLU GLY GLU ALA HIS GLU ARG SEQRES 12 A 195 ARG LEU PRO ALA VAL ARG SER ILE ASN GLY THR PHE GLN SEQRES 13 A 195 ALA ASP PHE PRO LEU GLY PRO ALA THR HIS GLY GLY THR SEQRES 14 A 195 TYR ARG CYS PHE GLY SER PHE ARG ASP ALA PRO TYR GLU SEQRES 15 A 195 TRP SER ASN SER SER ASP PRO LEU LEU VAL SER VAL THR FORMUL 2 HOH *53(H2 O) SHEET 1 A 3 SER A 9 LEU A 13 0 SHEET 2 A 3 VAL A 24 SER A 30 -1 O TRP A 29 N SER A 9 SHEET 3 A 3 SER A 60 ILE A 66 -1 O PHE A 64 N LEU A 26 SHEET 1 B 5 LEU A 17 LYS A 19 0 SHEET 2 B 5 LEU A 97 ILE A 102 1 O VAL A 100 N VAL A 18 SHEET 3 B 5 GLY A 75 SER A 82 -1 N GLY A 75 O MET A 99 SHEET 4 B 5 HIS A 36 ARG A 41 -1 N HIS A 40 O ARG A 78 SHEET 5 B 5 ASN A 47 LEU A 51 -1 O ASN A 47 N ARG A 41 SHEET 1 C 4 SER A 109 GLN A 113 0 SHEET 2 C 4 ASN A 123 SER A 130 -1 O SER A 129 N SER A 109 SHEET 3 C 4 PHE A 160 PRO A 168 -1 O LEU A 166 N VAL A 124 SHEET 4 C 4 VAL A 153 ARG A 154 -1 N VAL A 153 O GLN A 161 SHEET 1 D 5 THR A 117 VAL A 118 0 SHEET 2 D 5 LEU A 195 VAL A 199 1 O SER A 198 N VAL A 118 SHEET 3 D 5 GLY A 173 SER A 180 -1 N TYR A 175 O LEU A 195 SHEET 4 D 5 MET A 136 ARG A 141 -1 N SER A 140 O ARG A 176 SHEET 5 D 5 ARG A 148 PRO A 151 -1 O LEU A 150 N TYR A 137 SSBOND 1 CYS A 28 CYS A 79 1555 1555 2.04 SSBOND 2 CYS A 128 CYS A 177 1555 1555 2.05 CISPEP 1 LEU A 13 PRO A 14 0 4.65 CISPEP 2 GLY A 67 PRO A 68 0 -2.17 CISPEP 3 SER A 86 PRO A 87 0 8.97 CISPEP 4 GLN A 113 PRO A 114 0 6.18 CRYST1 51.232 62.851 65.934 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 0.019519 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015167 0.00000