HEADER IMMUNE SYSTEM 08-DEC-06 2O6R TITLE STRUCTURAL DIVERSITY OF THE HAGFISH VARIABLE LYMPHOCYTE RECEPTORS B61 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VARIABLE LYMPHOCYTE RECEPTOR B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LEUCINE-RICH REPEAT (LRR), RESIDUES 24-200; COMPND 5 SYNONYM: VARIABLE LYMPHOCYTE RECEPTOR B61; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EPTATRETUS BURGERI; SOURCE 3 ORGANISM_COMMON: INSHORE HAGFISH; SOURCE 4 ORGANISM_TAXID: 7764; SOURCE 5 GENE: VLRB; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HI5; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PVL1393 KEYWDS LEUCINE-RICH REPEAT PROTEIN, LRR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.O.LEE,H.M.KIM,S.C.OH REVDAT 5 30-OCT-24 2O6R 1 REMARK REVDAT 4 25-OCT-23 2O6R 1 REMARK REVDAT 3 24-FEB-09 2O6R 1 VERSN REVDAT 2 11-DEC-07 2O6R 1 JRNL REVDAT 1 26-DEC-06 2O6R 0 JRNL AUTH H.M.KIM,S.C.OH,K.J.LIM,J.KASAMATSU,J.Y.HEO,B.S.PARK,H.LEE, JRNL AUTH 2 O.J.YOO,M.KASAHARA,J.O.LEE JRNL TITL STRUCTURAL DIVERSITY OF THE HAGFISH VARIABLE LYMPHOCYTE JRNL TITL 2 RECEPTORS JRNL REF J.BIOL.CHEM. V. 282 6726 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17192264 JRNL DOI 10.1074/JBC.M608471200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1587740.850 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 8434 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 877 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1002 REMARK 3 BIN R VALUE (WORKING SET) : 0.1740 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1374 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 191 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.46000 REMARK 3 B22 (A**2) : -3.15000 REMARK 3 B33 (A**2) : 3.61000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.240 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 22.04 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2O6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97175 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8477 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 93.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 63.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 68.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 46.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1M10 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M TRIS-HCL, 0.2M REMARK 280 SODIUM CHLORIDE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295.0K 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 21.38700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.53000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.67750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.53000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.38700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.67750 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 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: 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 CYS A 163 CA - CB - SG ANGL. DEV. = -12.9 DEGREES REMARK 500 CYS A 163 N - CA - C ANGL. DEV. = 17.6 DEGREES REMARK 500 PRO A 164 C - N - CA ANGL. DEV. = -9.1 DEGREES REMARK 500 PRO A 199 C - N - CA ANGL. DEV. = 16.5 DEGREES REMARK 500 PRO A 199 C - N - CD ANGL. DEV. = -15.7 DEGREES REMARK 500 PRO A 199 N - CA - C ANGL. DEV. = 17.0 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 ASN A 61 -153.19 -121.21 REMARK 500 LEU A 98 49.43 -89.76 REMARK 500 ASN A 109 -154.54 -131.95 REMARK 500 LEU A 122 52.78 -92.63 REMARK 500 ASN A 133 -157.76 -139.41 REMARK 500 CYS A 163 -73.25 -70.00 REMARK 500 ASN A 176 40.47 -95.62 REMARK 500 PRO A 199 62.76 -52.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O6Q RELATED DB: PDB REMARK 900 INSHORE HAGFISH VARIABLE LYMPHOCYTE RECEPTOR A29 REMARK 900 RELATED ID: 2O6S RELATED DB: PDB REMARK 900 INSHORE HAGFISH VARIABLE LYMPHOCYTE RECEPTOR B59 DBREF 2O6R A 24 200 UNP Q4G1L2 Q4G1L2_EPTBU 24 200 SEQRES 1 A 177 CYS PRO SER ARG CYS SER CYS SER GLY THR GLU ILE ARG SEQRES 2 A 177 CYS ASN SER LYS GLY LEU THR SER VAL PRO THR GLY ILE SEQRES 3 A 177 PRO SER SER ALA THR ARG LEU GLU LEU GLU SER ASN LYS SEQRES 4 A 177 LEU GLN SER LEU PRO HIS GLY VAL PHE ASP LYS LEU THR SEQRES 5 A 177 GLN LEU THR LYS LEU SER LEU SER GLN ASN GLN ILE GLN SEQRES 6 A 177 SER LEU PRO ASP GLY VAL PHE ASP LYS LEU THR LYS LEU SEQRES 7 A 177 THR ILE LEU TYR LEU HIS GLU ASN LYS LEU GLN SER LEU SEQRES 8 A 177 PRO ASN GLY VAL PHE ASP LYS LEU THR GLN LEU LYS GLU SEQRES 9 A 177 LEU ALA LEU ASP THR ASN GLN LEU LYS SER VAL PRO ASP SEQRES 10 A 177 GLY ILE PHE ASP ARG LEU THR SER LEU GLN LYS ILE TRP SEQRES 11 A 177 LEU HIS THR ASN PRO TRP ASP CYS SER CYS PRO ARG ILE SEQRES 12 A 177 ASP TYR LEU SER ARG TRP LEU ASN LYS ASN SER GLN LYS SEQRES 13 A 177 GLU GLN GLY SER ALA LYS CYS SER GLY SER GLY LYS PRO SEQRES 14 A 177 VAL ARG SER ILE ILE CYS PRO THR FORMUL 2 HOH *191(H2 O) HELIX 1 1 SER A 162 ASN A 176 1 15 HELIX 2 2 PRO A 192 ILE A 196 5 5 SHEET 1 A 8 SER A 29 SER A 31 0 SHEET 2 A 8 GLU A 34 ARG A 36 -1 O ARG A 36 N SER A 29 SHEET 3 A 8 ARG A 55 GLU A 57 1 O ARG A 55 N ILE A 35 SHEET 4 A 8 LYS A 79 SER A 81 1 O LYS A 79 N LEU A 56 SHEET 5 A 8 ILE A 103 TYR A 105 1 O ILE A 103 N LEU A 80 SHEET 6 A 8 GLU A 127 ALA A 129 1 O GLU A 127 N LEU A 104 SHEET 7 A 8 LYS A 151 TRP A 153 1 O LYS A 151 N LEU A 128 SHEET 8 A 8 GLU A 180 GLN A 181 1 O GLN A 181 N ILE A 152 SSBOND 1 CYS A 24 CYS A 30 1555 1555 2.05 SSBOND 2 CYS A 28 CYS A 37 1555 1555 2.03 SSBOND 3 CYS A 161 CYS A 186 1555 1555 2.05 SSBOND 4 CYS A 163 CYS A 198 1555 1555 2.06 CRYST1 42.774 55.355 81.060 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 0.023379 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012337 0.00000