HEADER IMMUNE SYSTEM 23-APR-07 2YWZ TITLE STRUCTURE OF NEW ANTIGEN RECEPTOR VARIABLE DOMAIN FROM SHARKS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEW ANTIGEN RECEPTOR VARIABLE DOMAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORECTOLOBUS MACULATUS; SOURCE 3 ORGANISM_COMMON: SPOTTED WOBBEGONG; SOURCE 4 ORGANISM_TAXID: 168098; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGC KEYWDS IG VNAR, 1-A-11, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR V.A.STRELTSOV REVDAT 4 25-OCT-23 2YWZ 1 REMARK REVDAT 3 24-FEB-09 2YWZ 1 VERSN REVDAT 2 26-FEB-08 2YWZ 1 JRNL REVDAT 1 30-OCT-07 2YWZ 0 JRNL AUTH D.P.SIMMONS,V.A.STRELTSOV,O.DOLEZAL,P.J.HUDSON,A.M.COLEY, JRNL AUTH 2 M.FOLEY,D.F.PROLL,S.D.NUTTALL JRNL TITL SHARK IGNAR ANTIBODY MIMOTOPES TARGET A MURINE JRNL TITL 2 IMMUNOGLOBULIN THROUGH EXTENDED CDR3 LOOP STRUCTURES JRNL REF PROTEINS V. 71 119 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17932913 JRNL DOI 10.1002/PROT.21663 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 6303 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 + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 315 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 434 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 850 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.79000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : -2.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.64000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.263 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.224 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.421 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 866 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1174 ; 1.593 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 110 ; 7.222 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 33 ;32.150 ;23.939 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 152 ;19.490 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;16.474 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 136 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 630 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 370 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 577 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 69 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 36 ; 0.251 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.174 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 560 ; 0.712 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 889 ; 1.290 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 352 ; 1.882 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 285 ; 3.182 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2YWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000027239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 113.0 REMARK 200 PH : 6.50 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : AXCO MICROCAPILLARY FOCUSING REMARK 200 OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 180 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6619 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 18.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.00840 REMARK 200 R SYM (I) : 0.00840 REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : 0.55000 REMARK 200 FOR SHELL : 2.800 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: PDB ENTRY 1VES REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CACODYLATE, 36% MPEG 2000, PH REMARK 280 6.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 29.12600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.22100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.12600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.22100 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: 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 TYR A 92 -6.75 76.77 REMARK 500 SER A 96 -72.91 128.51 REMARK 500 LEU A 97 89.06 157.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VER RELATED DB: PDB REMARK 900 SIMILAR PROTEIN 12Y-1 REMARK 900 RELATED ID: 1VES RELATED DB: PDB REMARK 900 SIMILAR PROTEIN 12Y-2 REMARK 900 RELATED ID: 2COQ RELATED DB: PDB REMARK 900 SIMILAR PROTEIN 12A-9 REMARK 900 RELATED ID: 2YWY RELATED DB: PDB REMARK 900 SIMILAR PROTEIN 1-A-7 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE HAS BEEN DEPOSITED TO DATABASTHE GB WITH REMARK 999 ACCESSION CODE, DQ269923. DBREF 2YWZ A 1 111 UNP A9CBG5 A9CBG5_9CHON 1 111 SEQRES 1 A 111 ALA TRP VAL ASP GLN THR PRO ARG THR ILE THR LYS GLU SEQRES 2 A 111 THR GLY GLU SER LEU THR ILE LYS CYS VAL LEU LYS ASP SEQRES 3 A 111 HIS SER CYS GLY LEU SER SER THR THR TRP TYR ARG THR SEQRES 4 A 111 GLN LEU GLY SER THR ASN GLU LYS THR ILE SER ILE GLY SEQRES 5 A 111 GLY ARG TYR ASP GLU THR VAL ASP LYS GLY SER LYS SER SEQRES 6 A 111 PHE SER LEU ARG ILE SER ASP LEU ARG VAL GLU ASP SER SEQRES 7 A 111 GLY THR TYR LYS CYS GLN ALA ASP TYR SER PRO SER CYS SEQRES 8 A 111 TYR SER TYR PRO SER LEU GLU SER ALA VAL GLU GLY ALA SEQRES 9 A 111 GLY THR VAL LEU THR VAL LYS FORMUL 2 HOH *119(H2 O) HELIX 1 1 ARG A 74 ASP A 77 5 4 SHEET 1 A 4 TRP A 2 THR A 6 0 SHEET 2 A 4 LEU A 18 LYS A 25 -1 O LYS A 25 N TRP A 2 SHEET 3 A 4 SER A 65 ILE A 70 -1 O LEU A 68 N ILE A 20 SHEET 4 A 4 TYR A 55 ASP A 60 -1 N ASP A 60 O SER A 65 SHEET 1 B 5 THR A 9 LYS A 12 0 SHEET 2 B 5 THR A 106 VAL A 110 1 O THR A 109 N LYS A 12 SHEET 3 B 5 GLY A 79 TYR A 87 -1 N GLY A 79 O LEU A 108 SHEET 4 B 5 SER A 33 GLN A 40 -1 N SER A 33 O ASP A 86 SHEET 5 B 5 LYS A 47 THR A 48 -1 O LYS A 47 N ARG A 38 SHEET 1 C 4 THR A 9 LYS A 12 0 SHEET 2 C 4 THR A 106 VAL A 110 1 O THR A 109 N LYS A 12 SHEET 3 C 4 GLY A 79 TYR A 87 -1 N GLY A 79 O LEU A 108 SHEET 4 C 4 SER A 99 GLU A 102 -1 O SER A 99 N TYR A 87 SSBOND 1 CYS A 22 CYS A 83 1555 1555 2.06 SSBOND 2 CYS A 29 CYS A 91 1555 1555 2.06 CISPEP 1 THR A 6 PRO A 7 0 -10.00 CISPEP 2 SER A 96 LEU A 97 0 -3.27 CRYST1 58.252 50.442 46.731 90.00 104.43 90.00 C 1 2 1 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 0.017167 0.000000 0.004417 0.00000 SCALE2 0.000000 0.019825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022096 0.00000