HEADER ANTITOXIN 10-DEC-23 8V9Y TITLE X-RAY CRYSTAL STRUCTURE OF NANOBODY JGFN4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: JGFN4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELIDAE; SOURCE 3 ORGANISM_TAXID: 9835; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTITOXIN EXPDTA X-RAY DIFFRACTION AUTHOR K.SHI,N.MOLLER,H.AIHARA REVDAT 1 07-AUG-24 8V9Y 0 JRNL AUTH J.P.GALLANT,D.HICKS,K.SHI,N.H.MOELLER,B.HOPPE,E.W.LAKE, JRNL AUTH 2 C.BAEHR,M.PRAVETONI,H.AIHARA,A.M.LEBEAU JRNL TITL IDENTIFICATION AND BIOPHYSICAL CHARACTERIZATION OF A NOVEL JRNL TITL 2 DOMAIN-SWAPPED CAMELID ANTIBODY SPECIFIC FOR FENTANYL. JRNL REF J.BIOL.CHEM. V. 300 07502 2024 JRNL REFN ESSN 1083-351X JRNL PMID 38945452 JRNL DOI 10.1016/J.JBC.2024.107502 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 7988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 404 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 43.6300 - 4.8000 0.98 445 20 0.1951 0.2419 REMARK 3 2 4.7700 - 3.7900 0.90 381 22 0.1633 0.1787 REMARK 3 3 3.7800 - 3.3100 0.79 339 20 0.1630 0.2288 REMARK 3 4 3.3100 - 3.0000 1.00 412 25 0.1811 0.2657 REMARK 3 5 3.0000 - 2.7900 1.00 427 16 0.2029 0.2352 REMARK 3 6 2.7900 - 2.6200 1.00 408 24 0.1881 0.1955 REMARK 3 7 2.6200 - 2.4900 1.00 436 16 0.1957 0.1926 REMARK 3 8 2.4900 - 2.3800 0.98 405 18 0.2172 0.2521 REMARK 3 9 2.3800 - 2.2900 0.99 403 22 0.1971 0.2199 REMARK 3 10 2.2900 - 2.2100 0.85 358 29 0.1998 0.2554 REMARK 3 11 2.2100 - 2.1400 1.00 392 22 0.1874 0.2689 REMARK 3 12 2.1400 - 2.0800 0.99 413 17 0.2133 0.2598 REMARK 3 13 2.0800 - 2.0300 1.00 432 19 0.2075 0.1390 REMARK 3 14 2.0300 - 1.9800 0.99 389 22 0.1962 0.3000 REMARK 3 15 1.9800 - 1.9300 0.99 411 23 0.1732 0.2679 REMARK 3 16 1.9300 - 1.8900 0.91 374 17 0.2151 0.2945 REMARK 3 17 1.8900 - 1.8500 0.88 362 23 0.2080 0.2554 REMARK 3 18 1.8500 - 1.8200 0.76 302 22 0.1999 0.2015 REMARK 3 19 1.8200 - 1.7900 0.69 287 14 0.1970 0.3112 REMARK 3 20 1.7900 - 1.7600 0.52 208 13 0.2581 0.1640 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.92 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 : 0.003 872 REMARK 3 ANGLE : 0.599 1185 REMARK 3 CHIRALITY : 0.045 134 REMARK 3 PLANARITY : 0.004 154 REMARK 3 DIHEDRAL : 13.298 308 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 8V9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7992 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 43.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.27800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RD22EH53, G4.1 20 W/V POLYETHYLENE REMARK 280 GLYCOL MONOMETHYL ETHER 2000, 0.1 M TRIS PH8.5, 0.2 M REMARK 280 TRIMETHYLAMINE N-OXIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K 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 45.62150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.42900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.62150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.42900 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 239 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 GLN A 1 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 240 O HOH A 245 2.19 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 ALA A 24 70.89 -117.21 REMARK 500 THR A 28 97.69 -60.23 REMARK 500 SER A 29 30.27 -84.98 REMARK 500 ARG A 30 31.60 -144.65 REMARK 500 LEU A 100 -142.10 56.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 8V9Y A 0 119 PDB 8V9Y 8V9Y 0 119 SEQRES 1 A 120 MET GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ALA SEQRES 2 A 120 GLN ALA GLY GLY SER LEU GLN LEU SER CYS ALA ALA SER SEQRES 3 A 120 GLY SER THR SER ARG VAL ASN ALA MET GLY TRP TYR ARG SEQRES 4 A 120 GLN THR PRO GLY LYS GLU ARG GLU LEU VAL ALA ALA ILE SEQRES 5 A 120 ASP ARG SER GLY ALA THR VAL TYR SER GLU SER VAL ARG SEQRES 6 A 120 GLY ARG PHE THR ILE SER LYS ASN ASP ALA LYS ASN ILE SEQRES 7 A 120 VAL TRP LEU GLN MET ASN ASN LEU THR THR GLU ASP THR SEQRES 8 A 120 ALA VAL TYR TYR CYS ARG SER GLY VAL LEU GLY SER TRP SEQRES 9 A 120 GLY LEU GLY THR GLN VAL THR VAL SER SER HIS HIS HIS SEQRES 10 A 120 HIS HIS HIS FORMUL 2 HOH *61(H2 O) HELIX 1 AA1 THR A 86 THR A 90 5 5 SHEET 1 AA1 4 VAL A 5 SER A 7 0 SHEET 2 AA1 4 LEU A 18 ALA A 23 -1 O ALA A 23 N VAL A 5 SHEET 3 AA1 4 ILE A 77 MET A 82 -1 O LEU A 80 N LEU A 20 SHEET 4 AA1 4 PHE A 67 ASN A 72 -1 N THR A 68 O GLN A 81 SHEET 1 AA2 6 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 107 SER A 112 1 O THR A 110 N ALA A 12 SHEET 3 AA2 6 ALA A 91 SER A 97 -1 N TYR A 93 O THR A 107 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N TYR A 37 O TYR A 94 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O VAL A 58 N ALA A 50 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.03 CRYST1 91.243 26.858 36.962 90.00 106.99 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 0.010960 0.000000 0.003349 0.00000 SCALE2 0.000000 0.037233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028289 0.00000