HEADER IMMUNE SYSTEM 04-JAN-17 5UFF TITLE CRYSTAL STRUCTURE OF VARIABLE LYMPHOCYTE RECEPTOR (VLR) RBC36 WITH TITLE 2 FUCOSE(ALPHA-1-2)LACTOSE BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: RBC36; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PETROMYZON MARINUS; SOURCE 3 ORGANISM_COMMON: SEA LAMPREY; SOURCE 4 ORGANISM_TAXID: 7757; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS VARIABLE LYMPHOCYTE RECEPTORS, VLR, LEUCINE-RICH REPEAT, LRR, KEYWDS 2 ADAPTIVE IMMUNITY, IMMUNE SYSTEM, SEA LAMPREY, JAWLESS FISH, KEYWDS 3 RECEPTOR, GLYCAN BINDING, GLYCAN RECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR B.C.COLLINS,R.J.GUNN,T.R.MCKITRICK,B.R.HERRIN,R.D.CUMMINGS, AUTHOR 2 M.D.COOPER,I.A.WILSON REVDAT 5 04-OCT-23 5UFF 1 HETSYN REVDAT 4 29-JUL-20 5UFF 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 FORMUL LINK SITE ATOM REVDAT 3 11-DEC-19 5UFF 1 REMARK REVDAT 2 22-NOV-17 5UFF 1 JRNL REVDAT 1 18-OCT-17 5UFF 0 JRNL AUTH B.C.COLLINS,R.J.GUNN,T.R.MCKITRICK,R.D.CUMMINGS,M.D.COOPER, JRNL AUTH 2 B.R.HERRIN,I.A.WILSON JRNL TITL STRUCTURAL INSIGHTS INTO VLR FINE SPECIFICITY FOR BLOOD JRNL TITL 2 GROUP CARBOHYDRATES. JRNL REF STRUCTURE V. 25 1667 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 28988747 JRNL DOI 10.1016/J.STR.2017.09.003 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 11655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 560 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 39.8631 - 3.3919 0.98 2852 126 0.1748 0.2225 REMARK 3 2 3.3919 - 2.6924 0.98 2813 145 0.2327 0.2740 REMARK 3 3 2.6924 - 2.3521 0.97 2756 149 0.2740 0.3701 REMARK 3 4 2.3521 - 2.1371 0.94 2674 140 0.3703 0.4384 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.64 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 : 0.007 1694 REMARK 3 ANGLE : 1.117 2312 REMARK 3 CHIRALITY : 0.040 271 REMARK 3 PLANARITY : 0.005 290 REMARK 3 DIHEDRAL : 27.879 656 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 5UFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97840 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11758 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.137 REMARK 200 RESOLUTION RANGE LOW (A) : 39.865 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: PDB ENTRY 3E6J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11.4 MG/ML RBC36, 6.9 MM FUCOSE(ALPHA REMARK 280 -1-2)LACTOSE, 140 MM AMMONIUM CHLORIDE, 22% PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 23.75150 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 63 CD CE NZ REMARK 470 GLN A 98 CD OE1 NE2 REMARK 470 ASP A 118 CG OD1 OD2 REMARK 470 LYS A 124 CE NZ REMARK 470 LYS A 132 CE NZ REMARK 470 GLU A 135 CG CD OE1 OE2 REMARK 470 ARG A 138 CD NE CZ NH1 NH2 REMARK 470 GLU A 141 OE1 OE2 REMARK 470 GLN A 155 OE1 NE2 REMARK 470 LYS A 157 CD CE NZ REMARK 470 ARG A 185 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 216 NZ REMARK 470 GLU A 229 OE1 OE2 REMARK 470 LYS A 236 CG CD CE NZ 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 OE1 GLN A 60 O HOH A 401 2.04 REMARK 500 OG1 THR A 49 O HOH A 402 2.10 REMARK 500 O HOH A 403 O HOH A 424 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 423 O HOH A 447 2545 2.17 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 ASP A 58 52.97 77.69 REMARK 500 LEU A 72 56.54 -90.81 REMARK 500 ASN A 83 -157.66 -131.43 REMARK 500 THR A 106 56.41 72.43 REMARK 500 ASN A 107 -160.55 -129.67 REMARK 500 THR A 110 -58.67 -121.85 REMARK 500 ASN A 131 -154.95 -110.14 REMARK 500 ASN A 154 -129.65 -113.53 REMARK 500 GLN A 155 41.37 -148.24 REMARK 500 ASP A 205 67.95 -103.45 REMARK 500 LYS A 236 42.18 -148.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UEI RELATED DB: PDB REMARK 900 RELATED ID: 5UF1 RELATED DB: PDB REMARK 900 RELATED ID: 5UF4 RELATED DB: PDB REMARK 900 RELATED ID: 5UFB RELATED DB: PDB REMARK 900 RELATED ID: 5UFC RELATED DB: PDB REMARK 900 RELATED ID: 5UFD RELATED DB: PDB DBREF 5UFF A 22 237 PDB 5UFF 5UFF 22 237 SEQRES 1 A 216 CYS PRO SER GLN CYS SER CYS SER GLY THR THR VAL ASP SEQRES 2 A 216 CYS ARG SER LYS ARG HIS ALA SER VAL PRO ALA GLY ILE SEQRES 3 A 216 PRO THR ASN ALA GLN ILE LEU TYR LEU HIS ASP ASN GLN SEQRES 4 A 216 ILE THR LYS LEU GLU PRO GLY VAL PHE ASP SER LEU ILE SEQRES 5 A 216 ASN LEU LYS GLU LEU TYR LEU GLY SER ASN GLN LEU GLY SEQRES 6 A 216 ALA LEU PRO VAL GLY VAL PHE ASP SER LEU THR GLN LEU SEQRES 7 A 216 THR VAL LEU ASP LEU GLY THR ASN GLN LEU THR VAL LEU SEQRES 8 A 216 PRO SER ALA VAL PHE ASP ARG LEU VAL HIS LEU LYS GLU SEQRES 9 A 216 LEU PHE MET CYS CYS ASN LYS LEU THR GLU LEU PRO ARG SEQRES 10 A 216 GLY ILE GLU ARG LEU THR HIS LEU THR HIS LEU ALA LEU SEQRES 11 A 216 ASP GLN ASN GLN LEU LYS SER ILE PRO HIS GLY ALA PHE SEQRES 12 A 216 ASP ARG LEU SER SER LEU THR HIS ALA TYR LEU PHE GLY SEQRES 13 A 216 ASN PRO TRP ASP CYS GLU CYS ARG ASP ILE MET TYR LEU SEQRES 14 A 216 ARG ASN TRP VAL ALA ASP HIS THR SER ILE ALA MET ARG SEQRES 15 A 216 TRP ASP GLY LYS ALA VAL ASN ASP PRO ASP SER ALA LYS SEQRES 16 A 216 CYS ALA GLY THR ASN THR PRO VAL ARG ALA VAL THR GLU SEQRES 17 A 216 ALA SER THR SER PRO SER LYS CYS HET BGC B 1 12 HET GAL B 2 11 HET FUC B 3 10 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 FUC C6 H12 O5 FORMUL 3 HOH *61(H2 O) HELIX 1 AA1 GLY A 139 LEU A 143 5 5 HELIX 2 AA2 CYS A 184 ASP A 186 5 3 HELIX 3 AA3 ILE A 187 HIS A 197 1 11 HELIX 4 AA4 PRO A 223 VAL A 227 5 5 SHEET 1 AA110 SER A 27 SER A 29 0 SHEET 2 AA110 THR A 32 ASP A 34 -1 O ASP A 34 N SER A 27 SHEET 3 AA110 ILE A 53 TYR A 55 1 O ILE A 53 N VAL A 33 SHEET 4 AA110 GLU A 77 TYR A 79 1 O GLU A 77 N LEU A 54 SHEET 5 AA110 VAL A 101 ASP A 103 1 O VAL A 101 N LEU A 78 SHEET 6 AA110 GLU A 125 PHE A 127 1 O GLU A 125 N LEU A 102 SHEET 7 AA110 HIS A 148 ALA A 150 1 O ALA A 150 N LEU A 126 SHEET 8 AA110 HIS A 172 TYR A 174 1 O TYR A 174 N LEU A 149 SHEET 9 AA110 ALA A 201 TRP A 204 1 O MET A 202 N ALA A 173 SHEET 10 AA110 ALA A 208 ASN A 210 -1 O VAL A 209 N ARG A 203 SSBOND 1 CYS A 22 CYS A 28 1555 1555 2.05 SSBOND 2 CYS A 26 CYS A 35 1555 1555 2.05 SSBOND 3 CYS A 129 CYS A 130 1555 1555 2.07 SSBOND 4 CYS A 182 CYS A 217 1555 1555 2.05 SSBOND 5 CYS A 184 CYS A 237 1555 1555 2.04 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.40 LINK O2 GAL B 2 C1 FUC B 3 1555 1555 1.39 CRYST1 39.969 47.503 57.276 90.00 85.69 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 0.025019 0.000000 -0.001884 0.00000 SCALE2 0.000000 0.021051 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017509 0.00000