HEADER IMMUNE SYSTEM 20-DEC-22 8HT3 TITLE CRYSTAL STRUCTURE OF IMMUNOGLOBULIN NEW ANTIGEN RECEPTOR VARIABLE TITLE 2 DOMAIN FROM OKAMEJEI KENOJEI 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: OKAMEJEI KENOJEI; SOURCE 3 ORGANISM_TAXID: 432798; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, RAY VNAR., IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.WEN,P.LI,Y.BI REVDAT 2 24-JAN-24 8HT3 1 JRNL REVDAT 1 05-JUL-23 8HT3 0 JRNL AUTH J.WEN,J.GONG,P.LI,P.DENG,M.SUN,Y.WU,C.TIAN,H.WANG,Y.BI JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF IGNAR AND VNAR JRNL TITL 2 REPERTOIRE FROM THE OCELLATE SPOT SKATE (OKAMEJEI KENOJEI) JRNL REF FRONT MAR SCI V. 10 83744 2023 JRNL DOI 10.3389/FMARS.2023.1183744 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4024 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.140 REMARK 3 FREE R VALUE TEST SET COUNT : 408 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 14.0500 - 3.5900 1.00 1246 144 0.1805 0.2335 REMARK 3 2 3.5900 - 2.8600 1.00 1208 136 0.2003 0.2456 REMARK 3 3 2.8600 - 2.5000 0.99 1162 128 0.2140 0.3078 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 825 REMARK 3 ANGLE : 0.514 1118 REMARK 3 CHIRALITY : 0.038 126 REMARK 3 PLANARITY : 0.004 143 REMARK 3 DIHEDRAL : 17.286 117 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 8HT3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300034263. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4028 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 14.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.02776 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 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: MRBUMP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE/0.1 REMARK 280 M TRIS PH 8.0/26% W/V PEG4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 35.06950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.06950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 21.95050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.10650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.95050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.10650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.06950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.95050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.10650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.06950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.95050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.10650 REMARK 290 SMTRY3 8 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 ALA A 79 -178.02 -172.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HT3 A 1 104 PDB 8HT3 8HT3 1 104 SEQRES 1 A 104 VAL HIS VAL ALA GLN THR PRO ARG SER ALA THR LYS GLU SEQRES 2 A 104 SER GLY GLU THR LEU THR ILE ASN CYS ALA LEU ARG ASP SEQRES 3 A 104 THR SER TYR GLY LEU HIS SER THR ALA TRP TYR ARG GLN SEQRES 4 A 104 THR PRO GLY GLN SER ARG ARG ASP GLN LEU THR ILE GLY SEQRES 5 A 104 GLY ARG TYR VAL LYS THR VAL ASN LYS PRO GLN LYS THR SEQRES 6 A 104 PHE SER LEU GLN ILE ARG ASN LEU VAL VAL GLU ASP THR SEQRES 7 A 104 ALA THR TYR THR CYS ARG GLY TRP VAL GLY GLY ARG GLU SEQRES 8 A 104 GLY TYR GLU GLY ALA GLY THR LYS LEU THR VAL LYS PRO FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 VAL A 74 THR A 78 5 5 SHEET 1 AA1 4 HIS A 2 THR A 6 0 SHEET 2 AA1 4 LEU A 18 ARG A 25 -1 O ASN A 21 N THR A 6 SHEET 3 AA1 4 THR A 65 ILE A 70 -1 O PHE A 66 N CYS A 22 SHEET 4 AA1 4 TYR A 55 ASN A 60 -1 N ASN A 60 O THR A 65 SHEET 1 AA2 5 SER A 9 GLU A 13 0 SHEET 2 AA2 5 THR A 98 LYS A 103 1 O LYS A 103 N LYS A 12 SHEET 3 AA2 5 ALA A 79 TRP A 86 -1 N ALA A 79 O LEU A 100 SHEET 4 AA2 5 SER A 33 GLN A 39 -1 N GLN A 39 O THR A 80 SHEET 5 AA2 5 ASP A 47 GLN A 48 -1 O ASP A 47 N ARG A 38 SHEET 1 AA3 4 SER A 9 GLU A 13 0 SHEET 2 AA3 4 THR A 98 LYS A 103 1 O LYS A 103 N LYS A 12 SHEET 3 AA3 4 ALA A 79 TRP A 86 -1 N ALA A 79 O LEU A 100 SHEET 4 AA3 4 GLY A 92 GLU A 94 -1 O TYR A 93 N GLY A 85 SSBOND 1 CYS A 22 CYS A 83 1555 1555 2.03 CISPEP 1 THR A 6 PRO A 7 0 -1.11 CRYST1 43.901 72.213 70.139 90.00 90.00 90.00 C 2 2 21 8 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 0.022778 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014257 0.00000