HEADER ANTITOXIN 10-DEC-23 8V9Z TITLE X-RAY CRYSTAL STRUCTURE OF JGFN4 N76D COMPLEXED WITH FENTANYL IN TITLE 2 MONOMER FORM 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 8V9Z 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 11084 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 516 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 43.5100 - 2.5400 0.97 2737 125 0.1925 0.2336 REMARK 3 2 2.5400 - 2.0200 0.97 2646 135 0.2687 0.2772 REMARK 3 3 2.0200 - 1.7600 0.96 2601 124 0.3014 0.3311 REMARK 3 4 1.7600 - 1.6000 0.95 2584 132 0.4204 0.4698 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 46.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.33 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 : 0.005 884 REMARK 3 ANGLE : 0.670 1188 REMARK 3 CHIRALITY : 0.048 133 REMARK 3 PLANARITY : 0.006 153 REMARK 3 DIHEDRAL : 14.576 319 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.9790 -10.2603 12.4187 REMARK 3 T TENSOR REMARK 3 T11: 0.0682 T22: 0.3145 REMARK 3 T33: 0.5603 T12: -0.0280 REMARK 3 T13: -0.1767 T23: 0.0594 REMARK 3 L TENSOR REMARK 3 L11: 4.7104 L22: 0.7125 REMARK 3 L33: 3.6915 L12: -0.9655 REMARK 3 L13: -1.5516 L23: 0.4135 REMARK 3 S TENSOR REMARK 3 S11: 0.1633 S12: 0.5012 S13: 0.4869 REMARK 3 S21: -0.1863 S22: 0.0014 S23: -0.1056 REMARK 3 S31: -0.3187 S32: -0.0328 S33: 0.0656 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1484 -9.8125 10.9769 REMARK 3 T TENSOR REMARK 3 T11: 0.2149 T22: 0.4262 REMARK 3 T33: 0.6391 T12: 0.0172 REMARK 3 T13: -0.0951 T23: 0.0393 REMARK 3 L TENSOR REMARK 3 L11: 0.7102 L22: 4.1919 REMARK 3 L33: 4.5555 L12: -0.5484 REMARK 3 L13: 0.6699 L23: 3.3339 REMARK 3 S TENSOR REMARK 3 S11: 0.1343 S12: 0.0988 S13: 0.3160 REMARK 3 S21: -0.6134 S22: 0.1562 S23: -0.4946 REMARK 3 S31: -0.5085 S32: 0.9508 S33: -0.4675 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.7336 -15.0222 18.6413 REMARK 3 T TENSOR REMARK 3 T11: 0.1593 T22: 0.2991 REMARK 3 T33: 0.4869 T12: -0.0141 REMARK 3 T13: -0.1165 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 3.3526 L22: 1.4620 REMARK 3 L33: 1.7572 L12: -1.0609 REMARK 3 L13: -1.4215 L23: 0.3102 REMARK 3 S TENSOR REMARK 3 S11: -0.0499 S12: -0.1132 S13: -0.1789 REMARK 3 S21: 0.0624 S22: -0.0060 S23: -0.1108 REMARK 3 S31: -0.0026 S32: 0.0757 S33: 0.0099 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.5392 -5.2046 17.2379 REMARK 3 T TENSOR REMARK 3 T11: 0.1978 T22: 0.3128 REMARK 3 T33: 0.6287 T12: -0.0453 REMARK 3 T13: -0.1167 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 9.2973 L22: 2.1082 REMARK 3 L33: 4.7374 L12: 0.9199 REMARK 3 L13: -2.5307 L23: 0.2372 REMARK 3 S TENSOR REMARK 3 S11: -0.1374 S12: 0.2023 S13: 0.8010 REMARK 3 S21: -0.0692 S22: 0.1345 S23: -0.2254 REMARK 3 S31: -0.3873 S32: 0.3729 S33: -0.0543 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 8V9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-23 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 EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11199 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 2.52500 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 (%): 25.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: J341, F09_10 0.1 M BUFFER SYSTEM 3, PH REMARK 280 8.5, 0.12 M MONOSACCHARIDES, 50 % V/V PRECIPITANT MIX 1, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 45.54900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.54900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.17900 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 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 327 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 HIS A 114 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 DBREF 8V9Z A 0 119 PDB 8V9Z 8V9Z 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 ASP 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 HET 7V7 A 201 25 HETNAM 7V7 N-PHENYL-N-[1-(2-PHENYLETHYL)PIPERIDIN-4-YL]PROPANAMIDE FORMUL 2 7V7 C22 H28 N2 O FORMUL 3 HOH *36(H2 O) HELIX 1 AA1 THR A 28 VAL A 31 5 4 HELIX 2 AA2 THR 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 25 N GLN A 3 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 ALA A 33 GLN A 39 -1 N TYR A 37 O TYR A 94 SHEET 5 AA2 6 GLU A 46 ASP A 52 -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 2.02 CRYST1 91.098 26.358 37.458 90.00 107.19 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 0.010977 0.000000 0.003396 0.00000 SCALE2 0.000000 0.037939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027945 0.00000