HEADER IMMUNE SYSTEM 26-AUG-19 6U50 TITLE ANTI-SUDAN EBOLAVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY SUDAN B TITLE 2 (SB) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-SUDAN EBOLAVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY COMPND 3 SUDAN B (SB); COMPND 4 CHAIN: C; 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: PECAN219 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 6U50 1 REMARK REVDAT 4 01-JAN-20 6U50 1 JRNL REVDAT 3 11-DEC-19 6U50 1 JRNL REVDAT 2 04-DEC-19 6U50 1 REMARK REVDAT 1 06-NOV-19 6U50 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15516 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1567 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 37.2700 - 3.5500 0.99 1370 158 0.1747 0.1831 REMARK 3 2 3.5500 - 2.8200 1.00 1300 145 0.1655 0.2159 REMARK 3 3 2.8200 - 2.4600 1.00 1293 141 0.1697 0.2070 REMARK 3 4 2.4600 - 2.2400 1.00 1265 144 0.1582 0.2470 REMARK 3 5 2.2400 - 2.0800 1.00 1259 142 0.1378 0.1892 REMARK 3 6 2.0800 - 1.9500 1.00 1275 147 0.1391 0.1892 REMARK 3 7 1.9500 - 1.8600 1.00 1246 141 0.1568 0.2415 REMARK 3 8 1.8600 - 1.7800 1.00 1240 133 0.1752 0.2444 REMARK 3 9 1.7800 - 1.7100 1.00 1260 144 0.1947 0.2572 REMARK 3 10 1.7100 - 1.6500 1.00 1252 140 0.2122 0.2998 REMARK 3 11 1.6500 - 1.6000 0.95 1189 132 0.2630 0.3313 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) : 0.209 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.229 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.46 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 : 0.009 893 REMARK 3 ANGLE : 0.961 1210 REMARK 3 CHIRALITY : 0.085 130 REMARK 3 PLANARITY : 0.005 161 REMARK 3 DIHEDRAL : 13.636 334 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 6U50 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_1000243886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15558 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 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) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 6U51 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37.5% PRECIPITANT MIX (2-METHYL-2,4 REMARK 280 -PENTANEDIOL, POLYETHYLENE GLYCOL [PEG] 1000, PEG 3350), 0.1 M REMARK 280 AMINO ACIDS MIX (GLUTAMATE, ALANINE, GLYCINE, LYSINE, SERINE), REMARK 280 0.1 M HEPES/MOPS PH 7.5 {MOLECULAR DIMENSIONS MORPHEUS HT-96 REMARK 280 CONDITION H8}, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 28.45933 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 56.91867 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 56.91867 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 28.45933 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: C 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 C 1 REMARK 465 GLY C 26 REMARK 465 ALA C 27 REMARK 465 PHE C 28 REMARK 465 PHE C 29 REMARK 465 ARG C 30 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 C 91 169.95 176.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD C 201 DBREF 6U50 C 1 120 PDB 6U50 6U50 1 120 SEQRES 1 C 120 GLN VAL LYS LEU GLN GLN SER GLY GLY GLY SER VAL GLN SEQRES 2 C 120 GLU GLY GLY SER LEU ARG LEU SER CYS ALA SER SER GLY SEQRES 3 C 120 ALA PHE PHE ARG ALA GLY PRO MET GLY TRP TYR ARG ARG SEQRES 4 C 120 ALA PRO GLY ASN GLU ARG GLU LEU VAL ALA GLY ILE SER SEQRES 5 C 120 ARG ASN GLY ARG THR ILE TYR ALA PRO SER LEU LYS ASP SEQRES 6 C 120 ARG PHE THR ILE SER ARG ASP ASP ASP ASN ASN ILE LEU SEQRES 7 C 120 TYR LEU GLN MET SER ASP LEU THR PRO GLY ASP THR ALA SEQRES 8 C 120 VAL TYR TYR CYS ASN LEU ASN VAL ARG THR ALA VAL ALA SEQRES 9 C 120 GLY ARG ASN ASP TYR TRP GLY GLN GLY THR GLN VAL THR SEQRES 10 C 120 VAL SER SER HET MPD C 201 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD C6 H14 O2 FORMUL 3 HOH *86(H2 O) HELIX 1 AA1 PRO C 61 LYS C 64 5 4 HELIX 2 AA2 THR C 86 THR C 90 5 5 SHEET 1 AA1 4 LYS C 3 SER C 7 0 SHEET 2 AA1 4 LEU C 18 SER C 25 -1 O ALA C 23 N GLN C 5 SHEET 3 AA1 4 ILE C 77 MET C 82 -1 O LEU C 78 N CYS C 22 SHEET 4 AA1 4 PHE C 67 ASP C 72 -1 N ASP C 72 O ILE C 77 SHEET 1 AA2 6 GLY C 10 GLN C 13 0 SHEET 2 AA2 6 THR C 114 SER C 119 1 O SER C 119 N VAL C 12 SHEET 3 AA2 6 ALA C 91 ARG C 100 -1 N TYR C 93 O THR C 114 SHEET 4 AA2 6 MET C 34 ARG C 39 -1 N TYR C 37 O TYR C 94 SHEET 5 AA2 6 GLU C 46 ILE C 51 -1 O ILE C 51 N MET C 34 SHEET 6 AA2 6 THR C 57 TYR C 59 -1 O ILE C 58 N GLY C 50 SHEET 1 AA3 4 GLY C 10 GLN C 13 0 SHEET 2 AA3 4 THR C 114 SER C 119 1 O SER C 119 N VAL C 12 SHEET 3 AA3 4 ALA C 91 ARG C 100 -1 N TYR C 93 O THR C 114 SHEET 4 AA3 4 ARG C 106 TRP C 110 -1 O TYR C 109 N LEU C 97 SSBOND 1 CYS C 22 CYS C 95 1555 1555 2.07 SITE 1 AC1 6 PRO C 33 MET C 34 TYR C 37 GLY C 50 SITE 2 AC1 6 ASN C 96 HOH C 333 CRYST1 47.839 47.839 85.378 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 0.020903 0.012069 0.000000 0.00000 SCALE2 0.000000 0.024137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011713 0.00000