HEADER IMMUNE SYSTEM 18-DEC-15 5FFL TITLE CRYSTAL STRUCTURE OF MOUSE CD300LF AT 1.6 ANGSTROMS RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD300 ANTIGEN-LIKE FAMILY MEMBER F; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RANKL RESIDUES 156-316; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS CD300LF, CD300F, CLM-1, CLM1, IREM-1, IREM1, IGSF13, LMIR3, NKIR, KEYWDS 2 INHIBITORY RECEPTOR, IG SUPERFAMILY, CD300 MOLECULE-LIKE FAMILY KEYWDS 3 MEMBER F, IMMUNOGLOBULIN SUPERFAMILY MEMBER, CELL SURFACE RECEPTOR, KEYWDS 4 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.A.NELSON,D.H.FREMONT REVDAT 4 27-SEP-23 5FFL 1 REMARK REVDAT 3 22-NOV-17 5FFL 1 JRNL REMARK REVDAT 2 07-SEP-16 5FFL 1 JRNL REVDAT 1 31-AUG-16 5FFL 0 JRNL AUTH R.C.ORCHARD,C.B.WILEN,J.G.DOENCH,M.T.BALDRIDGE,B.T.MCCUNE, JRNL AUTH 2 Y.C.LEE,S.LEE,S.M.PRUETT-MILLER,C.A.NELSON,D.H.FREMONT, JRNL AUTH 3 H.W.VIRGIN JRNL TITL DISCOVERY OF A PROTEINACEOUS CELLULAR RECEPTOR FOR A JRNL TITL 2 NOROVIRUS. JRNL REF SCIENCE V. 353 933 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27540007 JRNL DOI 10.1126/SCIENCE.AAF1220 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 13654 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1364 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 19.1926 - 3.4450 0.91 1256 139 0.1422 0.1611 REMARK 3 2 3.4450 - 2.7370 0.95 1249 138 0.1551 0.1855 REMARK 3 3 2.7370 - 2.3917 0.97 1259 141 0.1588 0.2085 REMARK 3 4 2.3917 - 2.1734 0.97 1247 137 0.1667 0.2035 REMARK 3 5 2.1734 - 2.0178 0.98 1238 138 0.1523 0.2102 REMARK 3 6 2.0178 - 1.8989 0.98 1254 140 0.1653 0.2200 REMARK 3 7 1.8989 - 1.8039 0.99 1244 138 0.1757 0.2259 REMARK 3 8 1.8039 - 1.7254 0.99 1245 139 0.2248 0.2868 REMARK 3 9 1.7254 - 1.6590 0.97 1234 136 0.2601 0.3297 REMARK 3 10 1.6590 - 1.6018 0.84 1064 118 0.3124 0.3658 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.82 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 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 : 0.008 941 REMARK 3 ANGLE : 1.102 1275 REMARK 3 CHIRALITY : 0.068 136 REMARK 3 PLANARITY : 0.006 159 REMARK 3 DIHEDRAL : 15.073 571 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 5FFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8000 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) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49700 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: PHASER 2.6.0 REMARK 200 STARTING MODEL: 1XED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% (V/V) 2-METHYL-2,4-PENTANEDIOL, 50 REMARK 280 MM SODIUM CHLORIDE, 120 MM TRIS-HCL AT PH 7.25, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 13.81650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.25800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.67350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.25800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.81650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.67350 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 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL 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 368 O HOH A 391 2.06 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 GLN A 15 -1.19 71.68 REMARK 500 ASP A 30 31.52 -98.70 REMARK 500 ASN A 60 -122.79 53.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 94 O REMARK 620 2 GLY A 96 O 88.3 REMARK 620 3 ASP A 98 OD1 82.3 105.1 REMARK 620 4 EPE A 201 O3S 175.7 89.7 94.5 REMARK 620 5 HOH A 395 O 89.1 156.1 98.1 94.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 204 DBREF 5FFL A 1 112 UNP Q6SJQ7 CLM1_MOUSE 20 131 SEQADV 5FFL MET A 0 UNP Q6SJQ7 INITIATING METHIONINE SEQRES 1 A 113 MET GLU ASP PRO VAL THR GLY PRO GLU GLU VAL SER GLY SEQRES 2 A 113 GLN GLU GLN GLY SER LEU THR VAL GLN CYS ARG TYR THR SEQRES 3 A 113 SER GLY TRP LYS ASP TYR LYS LYS TYR TRP CYS GLN GLY SEQRES 4 A 113 VAL PRO GLN ARG SER CYS LYS THR LEU VAL GLU THR ASP SEQRES 5 A 113 ALA SER GLU GLN LEU VAL LYS LYS ASN ARG VAL SER ILE SEQRES 6 A 113 ARG ASP ASN GLN ARG ASP PHE ILE PHE THR VAL THR MET SEQRES 7 A 113 GLU ASP LEU ARG MET SER ASP ALA GLY ILE TYR TRP CYS SEQRES 8 A 113 GLY ILE THR LYS GLY GLY LEU ASP PRO MET PHE LYS VAL SEQRES 9 A 113 THR VAL ASN ILE GLY PRO VAL PRO THR HET EPE A 201 32 HET NA A 202 1 HET MPD A 203 22 HET MPD A 204 22 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM NA SODIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S FORMUL 3 NA NA 1+ FORMUL 4 MPD 2(C6 H14 O2) FORMUL 6 HOH *112(H2 O) HELIX 1 AA1 SER A 26 LYS A 29 5 4 HELIX 2 AA2 PRO A 40 CYS A 44 5 5 HELIX 3 AA3 ARG A 81 ALA A 85 5 5 SHEET 1 AA1 5 VAL A 4 THR A 5 0 SHEET 2 AA1 5 LEU A 18 TYR A 24 -1 O ARG A 23 N THR A 5 SHEET 3 AA1 5 ILE A 72 MET A 77 -1 O VAL A 75 N VAL A 20 SHEET 4 AA1 5 VAL A 62 ASN A 67 -1 N ASN A 67 O ILE A 72 SHEET 5 AA1 5 VAL A 57 LYS A 59 -1 N LYS A 59 O VAL A 62 SHEET 1 AA2 5 GLU A 9 GLN A 13 0 SHEET 2 AA2 5 MET A 100 GLY A 108 1 O ASN A 106 N VAL A 10 SHEET 3 AA2 5 GLY A 86 ILE A 92 -1 N GLY A 86 O VAL A 105 SHEET 4 AA2 5 LYS A 33 GLN A 37 -1 N TYR A 34 O GLY A 91 SHEET 5 AA2 5 LYS A 45 GLU A 49 -1 O LYS A 45 N GLN A 37 SSBOND 1 CYS A 22 CYS A 90 1555 1555 2.05 SSBOND 2 CYS A 36 CYS A 44 1555 1555 2.04 LINK O LYS A 94 NA NA A 202 1555 1555 2.35 LINK O GLY A 96 NA NA A 202 1555 1555 2.35 LINK OD1 ASP A 98 NA NA A 202 1555 1555 2.31 LINK O3S EPE A 201 NA NA A 202 1555 1555 2.43 LINK NA NA A 202 O HOH A 395 1555 1555 2.31 CISPEP 1 VAL A 39 PRO A 40 0 -1.65 SITE 1 AC1 14 GLN A 21 TYR A 34 ARG A 42 THR A 46 SITE 2 AC1 14 GLU A 49 THR A 93 GLY A 96 LEU A 97 SITE 3 AC1 14 ASP A 98 NA A 202 HOH A 305 HOH A 319 SITE 4 AC1 14 HOH A 382 HOH A 385 SITE 1 AC2 6 GLN A 21 LYS A 94 GLY A 96 ASP A 98 SITE 2 AC2 6 EPE A 201 HOH A 395 SITE 1 AC3 2 VAL A 39 SER A 43 SITE 1 AC4 3 ASP A 30 TYR A 31 HOH A 361 CRYST1 27.633 53.347 70.516 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 0.036189 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014181 0.00000