HEADER IMMUNE SYSTEM 26-AUG-19 6U53 TITLE ANTI-ZAIRE EBOLAVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY ZAIRE C TITLE 2 (ZC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-ZAIRE EBOLAVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY COMPND 3 ZAIRE C (ZC); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SEMI-SYNTHETIC SINGLE POT LIBRARY NOMAD 1 BASED UPON COMPND 7 LAMA GLAMA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PECAN73 KEYWDS ANTIBODY, NANOBODY, EBOLA, FILOVIRUS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.B.TAYLOR,L.J.SHERWOOD,P.J.HART,A.HAYHURST REVDAT 5 11-OCT-23 6U53 1 REMARK REVDAT 4 01-JAN-20 6U53 1 JRNL REVDAT 3 11-DEC-19 6U53 1 JRNL REVDAT 2 04-DEC-19 6U53 1 REMARK REVDAT 1 06-NOV-19 6U53 0 JRNL AUTH L.J.SHERWOOD,A.B.TAYLOR,P.J.HART,A.HAYHURST JRNL TITL PARATOPE DUALITY AND GULLYING ARE AMONG THE ATYPICAL JRNL TITL 2 RECOGNITION MECHANISMS USED BY A TRIO OF NANOBODIES TO JRNL TITL 3 DIFFERENTIATE EBOLAVIRUS NUCLEOPROTEINS. JRNL REF J.MOL.BIOL. V. 431 4848 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 31626803 JRNL DOI 10.1016/J.JMB.2019.10.005 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 68.2 REMARK 3 NUMBER OF REFLECTIONS : 13503 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1351 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 31.2400 - 3.2100 1.00 1915 214 0.1600 0.2113 REMARK 3 2 3.2100 - 2.5500 1.00 1816 201 0.2036 0.2749 REMARK 3 3 2.5500 - 2.2300 1.00 1782 198 0.2038 0.3010 REMARK 3 4 2.2300 - 2.0200 0.94 1675 187 0.2095 0.2698 REMARK 3 5 2.0200 - 1.8800 0.78 1375 153 0.2073 0.2697 REMARK 3 6 1.8800 - 1.7700 0.66 1164 129 0.2500 0.2979 REMARK 3 7 1.7700 - 1.6800 0.52 899 100 0.2887 0.3236 REMARK 3 8 1.6800 - 1.6100 0.39 690 76 0.2726 0.2858 REMARK 3 9 1.6100 - 1.5400 0.30 529 59 0.2765 0.4427 REMARK 3 10 1.5400 - 1.4900 0.18 307 34 0.3230 0.4194 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.205 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.87 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 : 0.009 1048 REMARK 3 ANGLE : 1.127 1429 REMARK 3 CHIRALITY : 0.085 146 REMARK 3 PLANARITY : 0.007 191 REMARK 3 DIHEDRAL : 15.564 375 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 6U53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243950. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-18 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-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13542 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 31.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 68.3 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 21.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: 6U51 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SODIUM/POTASSIUM TARTRATE, 0.2 M REMARK 280 LITHIUM SULFATE, 0.1M TRIS PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 18.90550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.20700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.20700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 9.45275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.20700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.20700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.35825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.20700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.20700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 9.45275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.20700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.20700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.35825 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 18.90550 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 LYS A 1 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 74 31.74 -144.98 REMARK 500 ASN A 76 48.99 38.69 REMARK 500 ALA A 99 -122.62 -138.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 6U53 A 1 123 PDB 6U53 6U53 1 123 SEQRES 1 A 123 LYS VAL GLN LEU GLN GLN SER GLY GLY GLY SER VAL THR SEQRES 2 A 123 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 123 SER ILE SER ASP PHE ALA ALA MET ALA TRP TYR ARG GLN SEQRES 4 A 123 ALA PRO GLY LYS GLU ARG ASP TRP VAL GLY THR ILE PHE SEQRES 5 A 123 SER ALA GLY ALA LEU LEU TYR ALA GLU PRO VAL LYS GLY SEQRES 6 A 123 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 A 123 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 A 123 VAL TYR TYR CYS ARG LEU TYR ALA GLU ALA ILE TYR TRP SEQRES 9 A 123 GLY GLN GLY THR GLN VAL THR VAL SER SER ALA ALA ALA SEQRES 10 A 123 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *66(H2 O) HELIX 1 AA1 SER A 27 PHE A 31 5 5 HELIX 2 AA2 LYS A 86 THR A 90 5 5 HELIX 3 AA3 SER A 114 HIS A 118 5 5 SHEET 1 AA1 4 LEU A 4 SER A 7 0 SHEET 2 AA1 4 LEU A 18 ALA A 24 -1 O ALA A 23 N GLN A 5 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 ARG A 71 -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 108 VAL A 112 1 O THR A 111 N VAL A 12 SHEET 3 AA2 6 ALA A 91 TYR A 98 -1 N TYR A 93 O THR A 108 SHEET 4 AA2 6 ALA A 33 GLN A 39 -1 N ALA A 33 O TYR A 98 SHEET 5 AA2 6 ASP A 46 PHE A 52 -1 O VAL A 48 N TRP A 36 SHEET 6 AA2 6 LEU A 57 TYR A 59 -1 O LEU A 58 N THR A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 108 VAL A 112 1 O THR A 111 N VAL A 12 SHEET 3 AA3 4 ALA A 91 TYR A 98 -1 N TYR A 93 O THR A 108 SHEET 4 AA3 4 ILE A 102 TRP A 104 -1 O TYR A 103 N LEU A 97 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.08 CRYST1 78.414 78.414 37.811 90.00 90.00 90.00 P 41 21 2 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 0.012753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026447 0.00000