HEADER IMMUNE SYSTEM 20-OCT-22 8H7N TITLE STRUCTURE OF NANOBODY 11A IN COMPLEX WITH TRIAZOPHOS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY 11A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELUS BACTRIANUS; SOURCE 3 ORGANISM_COMMON: BACTRIAN CAMEL; SOURCE 4 ORGANISM_TAXID: 9837; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NANOBODY, ORGANOPHOSPHORUS PESTICIDE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,J.D.LI,X.SHEN,Z.L.XU,Y.M.SUN REVDAT 1 25-OCT-23 8H7N 0 JRNL AUTH L.JIADONG,W.HONG JRNL TITL STRUCTURE OF NANOBODY 11A IN COMPLEX WITH TRIAZOPHOS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 451 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 36.5400 - 2.8700 1.00 3091 153 0.1911 0.2328 REMARK 3 2 2.8700 - 2.2800 1.00 2969 153 0.2398 0.2411 REMARK 3 3 2.0300 - 1.9900 1.00 2973 145 0.2555 0.2963 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) : 0.226 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.72 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 : 0.002 933 REMARK 3 ANGLE : 0.519 1263 REMARK 3 CHIRALITY : 0.044 138 REMARK 3 PLANARITY : 0.004 163 REMARK 3 DIHEDRAL : 10.226 341 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 8H7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300033008. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979176 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9567 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 42.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.94800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 8H7I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID, PH 3.5, 0.8 M REMARK 280 AMMONIUM SULFATE, PH 7.4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.99600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.99200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.99200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 10.99600 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 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 GLN A 119 REMARK 465 ALA A 120 REMARK 465 GLY A 121 REMARK 465 GLN A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 GLY A 129 REMARK 465 ALA A 130 REMARK 465 TYR A 131 REMARK 465 PRO A 132 REMARK 465 TYR A 133 REMARK 465 ASP A 134 REMARK 465 VAL A 135 REMARK 465 PRO A 136 REMARK 465 ASP A 137 REMARK 465 TYR A 138 REMARK 465 ALA A 139 REMARK 465 SER A 140 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 ARG A 29 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 100 CG OD1 OD2 REMARK 470 PHE A 101 CB CG CD1 CD2 CE1 CE2 CZ REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8H7I RELATED DB: PDB REMARK 900 RELATED ID: 8H7M RELATED DB: PDB REMARK 900 RELATED ID: 8H7R RELATED DB: PDB DBREF 8H7N A 1 140 PDB 8H7N 8H7N 1 140 SEQRES 1 A 140 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 140 PRO GLY GLY SER LEU ARG LEU SER CYS VAL GLY SER GLY SEQRES 3 A 140 ARG VAL ARG THR ILE ASN THR ALA GLY TRP TYR ARG GLN SEQRES 4 A 140 ALA PRO GLY GLN GLU PRO GLU PHE LEU ALA ARG ILE THR SEQRES 5 A 140 VAL GLY GLY THR THR SER TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 140 ARG PHE THR ILE SER ARG ASP LEU ALA LYS SER THR VAL SEQRES 7 A 140 TYR LEU GLN MET ASP TYR LEU LYS PRO GLU ASP THR ALA SEQRES 8 A 140 VAL TYR TYR CYS ASN ALA ASP PHE ASP PHE GLY SER ARG SEQRES 9 A 140 THR ALA TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 10 A 140 GLY GLN ALA GLY GLN HIS HIS HIS HIS HIS HIS GLY ALA SEQRES 11 A 140 TYR PRO TYR ASP VAL PRO ASP TYR ALA SER HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET WYW A 204 20 HET NA A 205 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM WYW TRIAZOPHOS HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL HETSYN WYW O,O-DIETHYL O-(1-PHENYL-1H-1,2,4-TRIAZOL-3-YL) HETSYN 2 WYW PHOSPHOROTHIOATE FORMUL 2 EDO 3(C2 H6 O2) FORMUL 5 WYW C12 H16 N3 O3 P S FORMUL 6 NA NA 1+ FORMUL 7 HOH *45(H2 O) HELIX 1 AA1 LYS A 86 THR A 90 5 5 SHEET 1 AA1 4 VAL A 2 SER A 7 0 SHEET 2 AA1 4 LEU A 18 GLY A 26 -1 O SER A 21 N SER A 7 SHEET 3 AA1 4 THR A 77 MET A 82 -1 O MET A 82 N LEU A 18 SHEET 4 AA1 4 PHE A 67 ASP A 72 -1 N THR A 68 O GLN A 81 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA2 6 ALA A 91 PHE A 99 -1 N TYR A 93 O THR A 111 SHEET 4 AA2 6 ILE A 31 GLN A 39 -1 N ASN A 32 O ASP A 98 SHEET 5 AA2 6 GLU A 46 THR A 52 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O SER A 58 N ARG A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA3 4 ALA A 91 PHE A 99 -1 N TYR A 93 O THR A 111 SHEET 4 AA3 4 ARG A 104 TRP A 107 -1 O ARG A 104 N PHE A 99 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.04 LINK OG SER A 21 NA NA A 205 1555 1555 3.04 CRYST1 84.386 84.386 32.988 90.00 90.00 120.00 P 31 2 1 6 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 0.011850 0.006842 0.000000 0.00000 SCALE2 0.000000 0.013684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030314 0.00000