HEADER IMMUNE SYSTEM 31-OCT-13 4NFD TITLE STRUCTURE OF PILR L108W MUTANT IN COMPLEX WITH SIALIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAIRED IMMUNOGLOBULIN-LIKE TYPE 2 RECEPTOR BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-150; COMPND 5 SYNONYM: ACTIVATING RECEPTOR PILR-BETA, CELL SURFACE RECEPTOR FDFACT; COMPND 6 ENGINEERED: YES; COMPND 7 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: FDFACT, PILR, PILRB, PP1551; 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 ACTIVATION RECEPTOR, CD99, SIALIC ACID, CELL KEYWDS 2 SURFACE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Q.LU,G.LU,J.QI,Y.LI,Y.ZHANG,H.WANG,Z.FAN,J.YAN,G.F.GAO REVDAT 4 08-NOV-23 4NFD 1 HETSYN REVDAT 3 29-JUL-20 4NFD 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 SITE REVDAT 2 17-SEP-14 4NFD 1 JRNL REVDAT 1 28-MAY-14 4NFD 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. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 566 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 41.4909 - 2.7118 0.98 2848 145 0.1597 0.1772 REMARK 3 2 2.7118 - 2.1525 1.00 2839 140 0.1755 0.2426 REMARK 3 3 2.1525 - 1.8804 1.00 2833 125 0.1658 0.2241 REMARK 3 4 1.8804 - 1.7080 0.98 2746 156 0.2113 0.2568 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 40.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.960 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) : -5.58470 REMARK 3 B22 (A**2) : -4.66270 REMARK 3 B33 (A**2) : 10.24740 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.10540 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 1072 REMARK 3 ANGLE : 1.140 1456 REMARK 3 CHIRALITY : 0.085 151 REMARK 3 PLANARITY : 0.006 185 REMARK 3 DIHEDRAL : 13.364 388 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): 9.3252 1.3773 15.0270 REMARK 3 T TENSOR REMARK 3 T11: 0.0564 T22: 0.0599 REMARK 3 T33: 0.0660 T12: 0.0003 REMARK 3 T13: 0.0018 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.0109 L22: 0.0197 REMARK 3 L33: 0.0294 L12: -0.0096 REMARK 3 L13: 0.0010 L23: -0.0003 REMARK 3 S TENSOR REMARK 3 S11: -0.0036 S12: 0.0044 S13: 0.0167 REMARK 3 S21: 0.0103 S22: -0.0063 S23: -0.0205 REMARK 3 S31: -0.0240 S32: -0.0104 S33: -0.0136 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 4NFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : 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 : 11851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 15.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : 0.34700 REMARK 200 FOR SHELL : 3.922 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: 4NFB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES SODIUM PH 7.5, 1.4M SODIUM REMARK 280 CITRATE TRIBASIC DEHYDRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 19.78550 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 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 HOH A 379 O HOH A 402 1.85 REMARK 500 O HOH A 379 O HOH A 386 1.87 REMARK 500 O HOH A 376 O HOH A 382 1.95 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 SER A 91 -168.54 -171.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NFB RELATED DB: PDB REMARK 900 STRUCTURE OF PILR REMARK 900 RELATED ID: 4NFC RELATED DB: PDB REMARK 900 STRUCTURE OF PILR DBREF 4NFD A 2 120 UNP Q9UKJ0 PILRB_HUMAN 32 150 SEQADV 4NFD MET A 1 UNP Q9UKJ0 EXPRESSION TAG SEQADV 4NFD TRP A 109 UNP Q9UKJ0 LEU 139 ENGINEERED MUTATION 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 ILE VAL PRO ASN VAL ARG ILE SEQRES 4 A 120 SER TRP ARG ARG GLY HIS PHE HIS GLY 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 GLU SER GLY SEQRES 7 A 120 PHE LEU ARG ILE SER ASN LEU ARG LYS GLU ASP GLN SER SEQRES 8 A 120 VAL TYR PHE CYS ARG VAL GLU LEU ASP THR ARG ARG SER SEQRES 9 A 120 GLY ARG GLN GLN TRP GLN SER ILE LYS GLY THR LYS LEU SEQRES 10 A 120 THR ILE THR HET SIA A 201 21 HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 2 SIA C11 H19 N O9 FORMUL 3 HOH *108(H2 O) HELIX 1 1 LYS A 61 VAL A 64 5 4 HELIX 2 2 ARG 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 SER A 24 N THR A 6 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 PHE A 68 O ARG A 81 SHEET 1 B 6 HIS A 10 ALA A 13 0 SHEET 2 B 6 THR A 115 ILE A 119 1 O LYS A 116 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 LYS A 116 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 -0.60 CRYST1 33.580 39.571 41.481 90.00 90.60 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 0.029780 0.000000 0.000312 0.00000 SCALE2 0.000000 0.025271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024109 0.00000