HEADER IMMUNE SYSTEM 31-OCT-13 4NFB TITLE STRUCTURE OF PAIRED IMMUNOGLOBULIN-LIKE TYPE 2 RECEPTOR (PILR ) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAIRED IMMUNOGLOBULIN-LIKE TYPE 2 RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-150; COMPND 5 SYNONYM: CELL SURFACE RECEPTOR FDF03, INHIBITORY RECEPTOR PILR-ALPHA; 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 GENE: PILR, PILRA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS IGV-LIKE, IMMUNE-RELATED INHIBITION RECEPTOR, HSV-1 GB, CELL SURFACE, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Q.LU,G.LU,J.QI,Y.LI,Y.ZHANG,H.WANG,Z.FAN,J.YAN,G.GAO REVDAT 3 20-MAR-24 4NFB 1 SEQADV REVDAT 2 17-SEP-14 4NFB 1 JRNL REVDAT 1 28-MAY-14 4NFB 0 JRNL AUTH Q.LU,G.LU,J.QI,H.WANG,Y.XUAN,Q.WANG,Y.LI,Y.ZHANG,C.ZHENG, JRNL AUTH 2 Z.FAN,J.YAN,G.F.GAO JRNL TITL PILR ALPHA AND PILR BETA HAVE A SIGLEC FOLD AND PROVIDE THE JRNL TITL 2 BASIS OF BINDING TO SIALIC ACID JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 8221 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24843130 JRNL DOI 10.1073/PNAS.1320716111 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 13610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 671 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 33.0766 - 2.7357 0.97 2710 153 0.1948 0.2152 REMARK 3 2 2.7357 - 2.1715 1.00 2690 131 0.1948 0.2355 REMARK 3 3 2.1715 - 1.8971 0.99 2635 140 0.1846 0.2064 REMARK 3 4 1.8971 - 1.7236 0.97 2558 127 0.1944 0.2532 REMARK 3 5 1.7236 - 1.6000 0.89 2346 120 0.2073 0.2392 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 : 0.42 REMARK 3 B_SOL : 59.58 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.680 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) : 7.86910 REMARK 3 B22 (A**2) : -5.03880 REMARK 3 B33 (A**2) : -2.83020 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 : 0.005 1024 REMARK 3 ANGLE : 0.959 1385 REMARK 3 CHIRALITY : 0.065 140 REMARK 3 PLANARITY : 0.003 177 REMARK 3 DIHEDRAL : 17.895 370 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): 10.1980 -8.3398 -6.4539 REMARK 3 T TENSOR REMARK 3 T11: 0.0881 T22: 0.1003 REMARK 3 T33: 0.0978 T12: -0.0036 REMARK 3 T13: 0.0086 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.7771 L22: 0.6812 REMARK 3 L33: 1.3328 L12: -0.3382 REMARK 3 L13: -0.2369 L23: 0.1821 REMARK 3 S TENSOR REMARK 3 S11: 0.0154 S12: 0.0360 S13: -0.0148 REMARK 3 S21: -0.0563 S22: -0.0328 S23: 0.0046 REMARK 3 S31: -0.1661 S32: -0.0038 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STARTING MODEL IS OBTAINED BY REMARK 3 SINGLE ISOMORPHOUS REPLACEMENT WITH A IODINE DERIVATIVE DATA. REMARK 4 REMARK 4 4NFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 1.00000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13899 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 29.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : 0.28000 REMARK 200 FOR SHELL : 5.920 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE TRIBASIC DEHYDRATE REMARK 280 PH 5.6, 20%(V/V) 2-PROPANOL, 20%(W/V) POLYETHYLENE GLYCOL 4,000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 20.27200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.57950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.16850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.57950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.27200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.16850 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: 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 30 76.47 15.63 REMARK 500 TRP A 71 144.84 -177.37 REMARK 500 ASN A 84 55.82 39.79 REMARK 500 SER A 91 -170.04 -175.71 REMARK 500 SER A 103 13.66 -143.42 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 TRP A 29 GLU A 30 130.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QFO RELATED DB: PDB REMARK 900 STRUCTURE OF SIGLEC-1 REMARK 900 RELATED ID: 1O7V RELATED DB: PDB REMARK 900 STRUCTURE OF SIGLEC-7 REMARK 900 RELATED ID: 2ZG2 RELATED DB: PDB REMARK 900 STRUCTURE OF SIGLEC-5 REMARK 900 RELATED ID: 4NFD RELATED DB: PDB REMARK 900 RELATED ID: 4NFC RELATED DB: PDB DBREF 4NFB A 2 120 UNP Q9UKJ1 PILRA_HUMAN 32 150 SEQADV 4NFB MET A 1 UNP Q9UKJ1 EXPRESSION TAG SEQRES 1 A 120 MET LEU TYR GLY VAL THR GLN PRO LYS HIS LEU SER ALA SEQRES 2 A 120 SER MET GLY GLY SER VAL GLU ILE PRO PHE SER PHE TYR SEQRES 3 A 120 TYR PRO TRP GLU LEU ALA THR ALA PRO ASP VAL ARG ILE SEQRES 4 A 120 SER TRP ARG ARG GLY HIS PHE HIS ARG GLN SER PHE TYR SEQRES 5 A 120 SER THR ARG PRO PRO SER ILE HIS LYS ASP TYR VAL ASN SEQRES 6 A 120 ARG LEU PHE LEU ASN TRP THR GLU GLY GLN LYS SER GLY SEQRES 7 A 120 PHE LEU ARG ILE SER ASN LEU GLN LYS GLN ASP GLN SER SEQRES 8 A 120 VAL TYR PHE CYS ARG VAL GLU LEU ASP THR ARG SER SER SEQRES 9 A 120 GLY ARG GLN GLN TRP GLN SER ILE GLU GLY THR LYS LEU SEQRES 10 A 120 SER ILE THR FORMUL 2 HOH *130(H2 O) HELIX 1 1 LYS A 61 VAL A 64 5 4 HELIX 2 2 GLN A 86 GLN A 90 5 5 SHEET 1 A 4 GLY A 4 THR A 6 0 SHEET 2 A 4 VAL A 19 TYR A 26 -1 O TYR A 26 N GLY A 4 SHEET 3 A 4 SER A 77 ILE A 82 -1 O LEU A 80 N ILE A 21 SHEET 4 A 4 LEU A 67 ASN A 70 -1 N ASN A 70 O PHE A 79 SHEET 1 B 6 HIS A 10 ALA A 13 0 SHEET 2 B 6 THR A 115 ILE A 119 1 O SER A 118 N LEU A 11 SHEET 3 B 6 SER A 91 ASP A 100 -1 N SER A 91 O LEU A 117 SHEET 4 B 6 ARG A 38 ARG A 43 -1 N SER A 40 O ARG A 96 SHEET 5 B 6 GLN A 49 SER A 53 -1 O PHE A 51 N TRP A 41 SHEET 6 B 6 SER A 58 ILE A 59 -1 O SER A 58 N SER A 53 SHEET 1 C 4 HIS A 10 ALA A 13 0 SHEET 2 C 4 THR A 115 ILE A 119 1 O SER A 118 N LEU A 11 SHEET 3 C 4 SER A 91 ASP A 100 -1 N SER A 91 O LEU A 117 SHEET 4 C 4 ARG A 106 GLN A 110 -1 O TRP A 109 N VAL A 97 CISPEP 1 ARG A 55 PRO A 56 0 -4.63 CRYST1 40.544 44.337 57.159 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 0.024665 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017495 0.00000