PDB Short entry for 3WO9 HEADER IMMUNE SYSTEM 20-DEC-13 3WO9 TITLE CRYSTAL STRUCTURE OF THE LAMPREY VARIABLE LYMPHOCYTE RECEPTOR C COMPND MOL_ID: 1; COMPND 2 MOLECULE: VARIABLE LYMPHOCYTE RECEPTOR C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VLRC ECTODOMAIN, UNP RESIDUES 25-246; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LETHENTERON CAMTSCHATICUM; SOURCE 3 ORGANISM_COMMON: JAPANESE LAMPREY; SOURCE 4 ORGANISM_TAXID: 980415; SOURCE 5 GENE: VLRC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C43(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-26(B) KEYWDS LEUCINE RICH REPEAT, IMMUNOLOGICAL RECEPTOR, MEMBRANE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.KANDA,Y.SUTOH,J.KASAMATSU,K.MAENAKA,M.KASAHARA,T.OSE REVDAT 2 08-NOV-23 3WO9 1 SEQADV REVDAT 1 05-MAR-14 3WO9 0 JRNL AUTH R.KANDA,Y.SUTOH,J.KASAMATSU,K.MAENAKA,M.KASAHARA,T.OSE JRNL TITL CRYSTAL STRUCTURE OF THE LAMPREY VARIABLE LYMPHOCYTE JRNL TITL 2 RECEPTOR C REVEALS AN UNUSUAL FEATURE IN ITS N-TERMINAL JRNL TITL 3 CAPPING MODULE. JRNL REF PLOS ONE V. 9 85875 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24465760 JRNL DOI 10.1371/JOURNAL.PONE.0085875 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 9769 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 476 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 37.4744 - 3.3167 1.00 3227 174 0.1739 0.2209 REMARK 3 2 3.3167 - 2.6328 1.00 3102 152 0.1951 0.2467 REMARK 3 3 2.6328 - 2.3001 0.97 2964 150 0.1805 0.2732 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.60 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 : 0.003 1740 REMARK 3 ANGLE : 0.762 2365 REMARK 3 CHIRALITY : 0.054 289 REMARK 3 PLANARITY : 0.002 308 REMARK 3 DIHEDRAL : 13.902 638 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 3WO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000096584. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : MIRRORS 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 : 9798 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 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) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2O6Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M POTASSIUM REMARK 280 PHOSPHATE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 51.07850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.61450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.07850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.61450 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 HIS A 3 REMARK 465 LYS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 SER A 15 REMARK 465 SER A 16 REMARK 465 GLY A 17 REMARK 465 GLU A 18 REMARK 465 ASN A 19 REMARK 465 LEU A 20 REMARK 465 TYR A 21 REMARK 465 PHE A 22 REMARK 465 GLN A 23 REMARK 465 GLY A 24 REMARK 465 ASN A 248 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 35 -101.66 -135.97 REMARK 500 ASN A 76 -157.08 -133.53 REMARK 500 ASN A 100 -154.32 -126.11 REMARK 500 GLN A 112 -10.67 73.88 REMARK 500 ASN A 124 -155.26 -113.18 REMARK 500 LEU A 137 59.74 -90.47 REMARK 500 ASN A 148 -148.09 -114.13 REMARK 500 GLN A 149 45.78 -142.91 REMARK 500 SER A 231 -146.74 -99.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 3WO9 A 27 248 UNP E0D2V6 E0D2V6_LAMJA 25 246 SEQADV 3WO9 MET A 1 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 ASN A 2 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 3 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 LYS A 4 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 5 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 6 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 7 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 8 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 9 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 10 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 11 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 12 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 13 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 14 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 SER A 15 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 SER A 16 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 GLY A 17 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 GLU A 18 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 ASN A 19 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 LEU A 20 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 TYR A 21 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 PHE A 22 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 GLN A 23 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 GLY A 24 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 HIS A 25 UNP E0D2V6 EXPRESSION TAG SEQADV 3WO9 MET A 26 UNP E0D2V6 EXPRESSION TAG SEQRES 1 A 248 MET ASN HIS LYS HIS HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 2 A 248 HIS SER SER GLY GLU ASN LEU TYR PHE GLN GLY HIS MET SEQRES 3 A 248 ALA CYS LEU ALA VAL GLY LYS ASP ASP ILE CYS THR CYS SEQRES 4 A 248 SER ASN LYS THR ASP SER SER PRO GLU THR VAL ASP CYS SEQRES 5 A 248 SER SER LYS LYS LEU THR ALA VAL PRO THR GLY ILE PRO SEQRES 6 A 248 ALA ASN THR GLU LYS LEU GLN LEU ASP PHE ASN GLN LEU SEQRES 7 A 248 ALA ASN ILE PRO ALA GLU ALA PHE HIS GLY LEU THR ARG SEQRES 8 A 248 LEU THR TYR LEU ALA LEU ASP TYR ASN GLN LEU GLN SER SEQRES 9 A 248 LEU PRO VAL GLY VAL PHE ASP GLN LEU ASN ASN LEU ASN SEQRES 10 A 248 GLU LEU ARG LEU GLN ASP ASN GLN LEU THR SER LEU PRO SEQRES 11 A 248 PRO GLY VAL PHE ASP SER LEU THR LYS LEU THR TYR LEU SEQRES 12 A 248 THR LEU SER GLN ASN GLN LEU GLN SER ILE PRO ALA GLY SEQRES 13 A 248 VAL PHE ASP LYS LEU THR ASN LEU ASN ARG LEU GLU LEU SEQRES 14 A 248 SER THR ASN GLN LEU GLN SER VAL PRO HIS GLY ALA PHE SEQRES 15 A 248 ASP SER LEU VAL ASN LEU GLU THR LEU HIS LEU GLU LEU SEQRES 16 A 248 ASN PRO TRP ASP CYS ALA CYS SER ASP ILE ILE TYR LEU SEQRES 17 A 248 ARG THR PHE ILE ALA LYS ASN THR ASP LYS ILE SER GLY SEQRES 18 A 248 MET GLU SER ALA GLN CYS ASN GLY THR SER THR ALA VAL SEQRES 19 A 248 LYS ASP VAL ASN THR GLU LYS ILE LYS ASN VAL THR CYS SEQRES 20 A 248 ASN FORMUL 2 HOH *101(H2 O) HELIX 1 1 ASP A 204 THR A 216 1 13 HELIX 2 2 ALA A 233 VAL A 237 5 5 SHEET 1 A 2 CYS A 28 ALA A 30 0 SHEET 2 A 2 LYS A 33 ASP A 34 -1 O LYS A 33 N LEU A 29 SHEET 1 B 8 THR A 38 SER A 40 0 SHEET 2 B 8 THR A 49 ASP A 51 -1 O ASP A 51 N THR A 38 SHEET 3 B 8 LYS A 70 GLN A 72 1 O LYS A 70 N VAL A 50 SHEET 4 B 8 TYR A 94 ALA A 96 1 O ALA A 96 N LEU A 71 SHEET 5 B 8 GLU A 118 ARG A 120 1 O ARG A 120 N LEU A 95 SHEET 6 B 8 TYR A 142 THR A 144 1 O TYR A 142 N LEU A 119 SHEET 7 B 8 ARG A 166 GLU A 168 1 O GLU A 168 N LEU A 143 SHEET 8 B 8 THR A 190 HIS A 192 1 O THR A 190 N LEU A 167 SSBOND 1 CYS A 28 CYS A 39 1555 1555 2.04 SSBOND 2 CYS A 37 CYS A 52 1555 1555 2.03 SSBOND 3 CYS A 200 CYS A 227 1555 1555 2.03 SSBOND 4 CYS A 202 CYS A 247 1555 1555 2.03 CRYST1 102.157 37.229 55.133 90.00 90.00 90.00 P 21 21 2 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 0.009789 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018138 0.00000