HEADER IMMUNE SYSTEM 10-AUG-22 8E1B TITLE CRYSTAL STRUCTURE OF NANOBODY VHH108 SPECIFIC FOR PA14 CIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY VHH108; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_ATCC_NUMBER: (DE3) RIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCOMB3X KEYWDS PSEUDOMONAS AERUGINOSA, NANOBODY VHH, IMMUNOGLOBULIN DOMAIN, CFTR KEYWDS 2 INHIBITORY FACTOR (CIF), IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.R.SIMARD,N.M.TAHER,A.K.MISHRA,D.R.MADDEN REVDAT 1 04-OCT-23 8E1B 0 JRNL AUTH A.R.SIMARD,D.R.MADDEN JRNL TITL CRYSTAL STRUCTURE OF NANOBODY VHH108 SPECIFIC FOR PA14 CIF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.VASYLIEVA,S.KITAMURA,J.DONG,B.BARNYCH,K.L.HVORECNY, REMARK 1 AUTH 2 D.R.MADDEN,S.J.GEE,D.W.WOLAN,C.MORISSEAU,B.D.HAMMOCK REMARK 1 TITL NANOBODY-BASED BINDING ASSAY FOR THE DISCOVERY OF POTENT REMARK 1 TITL 2 INHIBITORS OF CFTR INHIBITORY FACTOR (CIF). REMARK 1 REF ANAL CHIM ACTA V.1057 106 2019 REMARK 1 REFN ISSN 1873-4324 REMARK 1 PMID 30832908 REMARK 1 DOI 10.1016/J.ACA.2018.12.060 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14564 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 691 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 33.2000 - 2.8200 1.00 2920 142 0.1934 0.1765 REMARK 3 2 2.8200 - 2.2400 1.00 2771 141 0.2259 0.2592 REMARK 3 3 2.2400 - 1.9600 1.00 2733 139 0.2192 0.2365 REMARK 3 4 1.9600 - 1.7800 1.00 2736 138 0.2318 0.2791 REMARK 3 5 1.7800 - 1.6500 1.00 2713 131 0.3575 0.3934 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) : 0.275 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.856 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.05 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 : 0.007 908 REMARK 3 ANGLE : 0.836 1229 REMARK 3 CHIRALITY : 0.059 137 REMARK 3 PLANARITY : 0.007 160 REMARK 3 DIHEDRAL : 14.138 327 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: REMARK 3 THE BOUNDARIES FOR STRETCHES OF MISSING RESIDUES WERE DETERMINED REMARK 3 USING A COMPOSITE OMIT MAP WITH A ONE-SIGMA CUTOFF UNLESS REMARK 3 OTHERWISE STATED. POSITIVE ELECTRON-DENSITY PEAKS ARE OBSERVED REMARK 3 WHERE RESIDUES 74:76 OF CHAIN A WOULD BE LOCATED, BUT THE REMARK 3 PLACEMENT OF MAIN-CHAIN ATOMS COULD NOT BE RESOLVED. REMARK 3 REMARK 3 ATOMS MODELED WITH ZERO OCCUPANCY COULD NOT BE PLACED WITH REMARK 3 CONFIDENCE AND WERE SELECTED FOR ZERO-OCCUPANCY FLAGGING AFTER REMARK 3 MANUAL INSPECTION OF THE 2FO-FC MAP AT A 0.5-SIGMA CUTOFF. REMARK 3 REMARK 3 ALTHOUGH THE CORRELATION IS LOW, RESIDUES 30 AND 103 IN CHAIN A REMARK 3 HAVE REASONABLE CONCORDANCE WITH THE 2FO-FC MAP, ARE NOT ROTAMER REMARK 3 OUTLIERS, AND ARE DEVOID OF CLASHES WITH NEIGHBORING ATOMS. REMARK 4 REMARK 4 8E1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-20 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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920099 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 33.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05386 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 1.19200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.140 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: 4JVP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM THIOCYANATE, 20% (W/V) REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292.8K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 15.43550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.07350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.43550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.07350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 VAL A 4 REMARK 465 ASP A 31 REMARK 465 ASP A 32 REMARK 465 ARG A 33 REMARK 465 ILE A 74 REMARK 465 ALA A 75 REMARK 465 ASN A 76 REMARK 465 ASP A 105 REMARK 465 ARG A 106 REMARK 465 GLY A 128 REMARK 465 GLN A 129 REMARK 465 ALA A 130 REMARK 465 GLY A 131 REMARK 465 GLN A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 REMARK 465 HIS A 138 REMARK 465 GLY A 139 REMARK 465 ALA A 140 REMARK 465 TYR A 141 REMARK 465 PRO A 142 REMARK 465 TYR A 143 REMARK 465 ASP A 144 REMARK 465 VAL A 145 REMARK 465 PRO A 146 REMARK 465 ASP A 147 REMARK 465 TYR A 148 REMARK 465 ALA A 149 REMARK 465 SER A 150 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 29 OD1 ND2 REMARK 480 ARG A 55 CD NE CZ NH1 NH2 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 92 166.75 179.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 8E1B A 1 150 PDB 8E1B 8E1B 1 150 SEQRES 1 A 150 MET ALA GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 A 150 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS GLU ALA SEQRES 3 A 150 THR GLY ASN PHE ASP ASP ARG GLY ILE GLY TRP PHE ARG SEQRES 4 A 150 GLN ALA PRO GLY LYS GLU ARG GLU GLY ILE ALA CYS ILE SEQRES 5 A 150 THR THR ARG GLY ARG THR HIS TYR ALA GLU SER VAL GLU SEQRES 6 A 150 GLY ARG PHE THR ILE SER THR ASP ILE ALA ASN ASN ALA SEQRES 7 A 150 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 150 ALA VAL TYR TYR CYS ALA LYS ALA ILE ARG LEU THR THR SEQRES 9 A 150 ASP ARG THR GLN CYS VAL ALA PHE PRO GLY VAL SER TRP SEQRES 10 A 150 GLY ARG GLY THR GLN VAL THR VAL SER SER GLY GLN ALA SEQRES 11 A 150 GLY GLN HIS HIS HIS HIS HIS HIS GLY ALA TYR PRO TYR SEQRES 12 A 150 ASP VAL PRO ASP TYR ALA SER FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 LYS A 87 THR A 91 5 5 SHEET 1 AA1 4 LEU A 6 SER A 9 0 SHEET 2 AA1 4 LEU A 20 ALA A 26 -1 O GLU A 25 N VAL A 7 SHEET 3 AA1 4 ALA A 78 MET A 83 -1 O MET A 83 N LEU A 20 SHEET 4 AA1 4 PHE A 68 THR A 72 -1 N SER A 71 O TYR A 80 SHEET 1 AA2 6 GLY A 12 VAL A 14 0 SHEET 2 AA2 6 THR A 121 VAL A 125 1 O THR A 124 N GLY A 12 SHEET 3 AA2 6 ALA A 92 LEU A 102 -1 N TYR A 94 O THR A 121 SHEET 4 AA2 6 ILE A 35 GLN A 40 -1 N PHE A 38 O TYR A 95 SHEET 5 AA2 6 GLU A 47 ILE A 52 -1 O ALA A 50 N TRP A 37 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O HIS A 59 N CYS A 51 SHEET 1 AA3 4 GLY A 12 VAL A 14 0 SHEET 2 AA3 4 THR A 121 VAL A 125 1 O THR A 124 N GLY A 12 SHEET 3 AA3 4 ALA A 92 LEU A 102 -1 N TYR A 94 O THR A 121 SHEET 4 AA3 4 GLN A 108 ALA A 111 -1 O VAL A 110 N ILE A 100 SSBOND 1 CYS A 24 CYS A 96 1555 1555 2.03 SSBOND 2 CYS A 51 CYS A 109 1555 1555 2.04 CRYST1 30.871 112.147 33.198 90.00 90.00 90.00 P 21 21 2 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 0.032393 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030122 0.00000