HEADER IMMUNE SYSTEM 09-MAR-18 6CNW TITLE STRUCTURE OF HUMANIZED SINGLE DOMAIN ANTIBODY SD84 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMANIZED ANTIBODY SD84H; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYBRID; SOURCE 3 ORGANISM_TAXID: 37965; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK293FEXPI KEYWDS SINGLE DOMAIN ANTIBODY, HUMANIZATION, INFLUENZA, HEMAGGLUTININ, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.LUO,O.OBMOLOVA REVDAT 2 23-OCT-24 6CNW 1 REMARK REVDAT 1 14-NOV-18 6CNW 0 JRNL AUTH N.S.LAURSEN,R.H.E.FRIESEN,X.ZHU,M.JONGENEELEN,S.BLOKLAND, JRNL AUTH 2 J.VERMOND,A.VAN EIJGEN,C.TANG,H.VAN DIEPEN,G.OBMOLOVA, JRNL AUTH 3 M.VAN DER NEUT KOLFSCHOTEN,D.ZUIJDGEEST,R.STRAETEMANS, JRNL AUTH 4 R.M.B.HOFFMAN,T.NIEUSMA,J.PALLESEN,H.L.TURNER,S.M.BERNARD, JRNL AUTH 5 A.B.WARD,J.LUO,L.L.M.POON,A.P.TRETIAKOVA,J.M.WILSON, JRNL AUTH 6 M.P.LIMBERIS,R.VOGELS,B.BRANDENBURG,J.A.KOLKMAN,I.A.WILSON JRNL TITL UNIVERSAL PROTECTION AGAINST INFLUENZA INFECTION BY A JRNL TITL 2 MULTIDOMAIN ANTIBODY TO INFLUENZA HEMAGGLUTININ. JRNL REF SCIENCE V. 362 598 2018 JRNL REFN ESSN 1095-9203 JRNL PMID 30385580 JRNL DOI 10.1126/SCIENCE.AAQ0620 REMARK 2 REMARK 2 RESOLUTION. 0.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 0.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 3 NUMBER OF REFLECTIONS : 63552 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3179 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 24.4130 - 2.6156 0.99 3096 163 0.1479 0.1732 REMARK 3 2 2.6156 - 2.0764 0.99 3026 160 0.1334 0.1419 REMARK 3 3 2.0764 - 1.8140 0.99 2997 157 0.1278 0.1301 REMARK 3 4 1.8140 - 1.6482 0.99 2993 158 0.1294 0.1338 REMARK 3 5 1.6482 - 1.5301 0.99 3029 159 0.1215 0.1410 REMARK 3 6 1.5301 - 1.4399 0.99 2984 157 0.1132 0.1351 REMARK 3 7 1.4399 - 1.3678 1.00 2999 158 0.1138 0.1363 REMARK 3 8 1.3678 - 1.3082 1.00 3025 160 0.1122 0.1257 REMARK 3 9 1.3082 - 1.2579 0.99 3004 158 0.1032 0.0972 REMARK 3 10 1.2579 - 1.2145 1.00 3001 158 0.0974 0.1117 REMARK 3 11 1.2145 - 1.1765 1.00 3030 159 0.0968 0.1083 REMARK 3 12 1.1765 - 1.1429 1.00 2990 157 0.0936 0.1052 REMARK 3 13 1.1429 - 1.1128 1.00 2986 158 0.0919 0.1146 REMARK 3 14 1.1128 - 1.0856 1.00 3005 158 0.0936 0.1166 REMARK 3 15 1.0856 - 1.0610 1.00 3016 158 0.0998 0.1267 REMARK 3 16 1.0610 - 1.0384 1.00 3023 160 0.1065 0.1238 REMARK 3 17 1.0384 - 1.0176 1.00 2982 157 0.1171 0.1137 REMARK 3 18 1.0176 - 0.9984 0.91 2763 145 0.1298 0.1503 REMARK 3 19 0.9984 - 0.9806 0.70 2088 110 0.1501 0.1545 REMARK 3 20 0.9806 - 0.9640 0.56 1672 88 0.1759 0.1960 REMARK 3 21 0.9640 - 0.9484 0.42 1271 67 0.2039 0.2266 REMARK 3 22 0.9484 - 0.9338 0.30 891 47 0.2374 0.2233 REMARK 3 23 0.9338 - 0.9201 0.17 502 27 0.2873 0.1944 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) : 0.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 966 REMARK 3 ANGLE : 1.009 1304 REMARK 3 CHIRALITY : 0.088 138 REMARK 3 PLANARITY : 0.006 166 REMARK 3 DIHEDRAL : 22.263 347 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 6CNW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63610 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 REMARK 200 RESOLUTION RANGE LOW (A) : 26.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : 5.760 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 29.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.46 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.170 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 (%): 42.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M (NH4)2SO4, 0.1 M SODIUM ACETATE, REMARK 280 5% PEG 400, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 17.92500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.96250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.88750 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 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 312 O HOH A 363 1.98 REMARK 500 O HOH A 304 O HOH A 313 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 409 O HOH A 410 2545 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 207 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 207 DBREF 6CNW A 1 116 PDB 6CNW 6CNW 1 116 SEQRES 1 A 116 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 116 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 116 PHE THR PHE SER THR SER TRP MET TYR TRP LEU ARG GLN SEQRES 4 A 116 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE ASN SEQRES 5 A 116 THR ASP GLY GLY THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 116 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 A 116 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 A 116 VAL TYR TYR CYS ALA LYS ASP TRP GLY GLY PRO GLU PRO SEQRES 9 A 116 THR ARG GLY GLN GLY THR LEU VAL THR VAL SER SER HET ACT A 201 4 HET ACT A 202 4 HET ACT A 203 4 HET PEG A 204 7 HET PEG A 205 7 HET PEG A 206 7 HET PEG A 207 5 HETNAM ACT ACETATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 ACT 3(C2 H3 O2 1-) FORMUL 5 PEG 4(C4 H10 O3) FORMUL 9 HOH *122(H2 O) HELIX 1 AA1 THR A 28 SER A 32 5 5 HELIX 2 AA2 ASP A 61 LYS A 64 5 4 HELIX 3 AA3 ASN A 73 LYS A 75 5 3 HELIX 4 AA4 ARG A 86 THR A 90 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 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 ASP A 72 -1 N SER A 70 O TYR A 79 SHEET 1 AA2 6 LEU A 11 VAL A 12 0 SHEET 2 AA2 6 THR A 110 VAL A 114 1 O THR A 113 N VAL A 12 SHEET 3 AA2 6 ALA A 91 LYS A 97 -1 N TYR A 93 O THR A 110 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N LEU A 37 O TYR A 94 SHEET 5 AA2 6 LEU A 45 ILE A 51 -1 O VAL A 48 N TRP A 36 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O TYR A 58 N VAL A 50 SHEET 1 AA3 4 LEU A 11 VAL A 12 0 SHEET 2 AA3 4 THR A 110 VAL A 114 1 O THR A 113 N VAL A 12 SHEET 3 AA3 4 ALA A 91 LYS A 97 -1 N TYR A 93 O THR A 110 SHEET 4 AA3 4 THR A 105 ARG A 106 -1 O THR A 105 N LYS A 97 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.06 CISPEP 1 GLY A 101 PRO A 102 0 -0.30 SITE 1 AC1 3 PHE A 27 THR A 28 HOH A 347 SITE 1 AC2 5 THR A 57 TYR A 59 HOH A 325 HOH A 329 SITE 2 AC2 5 HOH A 359 SITE 1 AC3 6 ASP A 72 ASN A 73 SER A 74 PEG A 204 SITE 2 AC3 6 HOH A 303 HOH A 399 SITE 1 AC4 8 ASN A 52 GLY A 56 THR A 57 ACT A 203 SITE 2 AC4 8 PEG A 207 HOH A 302 HOH A 315 HOH A 396 SITE 1 AC5 5 ASN A 83 SER A 115 SER A 116 HOH A 332 SITE 2 AC5 5 HOH A 388 SITE 1 AC6 4 THR A 31 VAL A 50 TYR A 58 HOH A 306 SITE 1 AC7 3 THR A 53 PEG A 204 HOH A 349 CRYST1 54.570 54.570 35.850 90.00 90.00 90.00 P 41 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 0.018325 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027894 0.00000