HEADER IMMUNE SYSTEM 03-FEB-22 7R20 TITLE ANTI-ARC NANOBODY E5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-ARC NANOBODY E5; COMPND 3 CHAIN: B; 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(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NANOBODY, VHH, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.MARKUSSON,P.KURSULA REVDAT 3 31-JAN-24 7R20 1 REMARK REVDAT 2 29-JUN-22 7R20 1 JRNL REVDAT 1 01-JUN-22 7R20 0 JRNL AUTH S.MARKUSSON,E.I.HALLIN,H.J.BUSTAD,A.RAASAKKA,J.XU, JRNL AUTH 2 G.MURUGANANDAM,R.LORIS,A.MARTINEZ,C.R.BRAMHAM,P.KURSULA JRNL TITL HIGH-AFFINITY ANTI-ARC NANOBODIES PROVIDE TOOLS FOR JRNL TITL 2 STRUCTURAL AND FUNCTIONAL STUDIES. JRNL REF PLOS ONE V. 17 69281 2022 JRNL REFN ESSN 1932-6203 JRNL PMID 35671319 JRNL DOI 10.1371/JOURNAL.PONE.0269281 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3958 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 21512 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.210 REMARK 3 FREE R VALUE TEST SET COUNT : 1981 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 41.9800 - 3.4200 1.00 1564 159 0.1783 0.2156 REMARK 3 2 3.4200 - 2.7200 1.00 1450 145 0.1693 0.2108 REMARK 3 3 2.7200 - 2.3700 1.00 1437 146 0.1512 0.2046 REMARK 3 4 2.3700 - 2.1600 1.00 1417 145 0.1288 0.2032 REMARK 3 5 2.1600 - 2.0000 0.99 1386 140 0.1413 0.2185 REMARK 3 6 2.0000 - 1.8800 0.99 1401 143 0.1378 0.2248 REMARK 3 7 1.8800 - 1.7900 1.00 1396 141 0.1699 0.2444 REMARK 3 8 1.7900 - 1.7100 0.99 1356 137 0.2282 0.3011 REMARK 3 9 1.7100 - 1.6500 0.99 1377 141 0.2761 0.3655 REMARK 3 10 1.6500 - 1.5900 0.99 1376 139 0.3263 0.3888 REMARK 3 11 1.5900 - 1.5400 1.00 1376 139 0.3458 0.4019 REMARK 3 12 1.5400 - 1.4900 1.00 1384 141 0.4041 0.4345 REMARK 3 13 1.4900 - 1.4600 0.98 1340 138 0.4929 0.5193 REMARK 3 14 1.4600 - 1.4200 0.92 1271 127 0.5469 0.5420 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.257 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.713 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.08 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 : 0.012 1005 REMARK 3 ANGLE : 1.274 1361 REMARK 3 CHIRALITY : 0.096 140 REMARK 3 PLANARITY : 0.008 175 REMARK 3 DIHEDRAL : 16.092 364 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 7R20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS FEB 5, 2021 REMARK 200 DATA SCALING SOFTWARE : XSCALE FEB 5, 2021 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 201623 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 41.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3. REMARK 200 STARTING MODEL: 5HVG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.26 M (NH4)2SO4, 0.1 M LISO4 AND 0.1 REMARK 280 M TRIS-HCL PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 51.87500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.95000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.81250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.95000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.93750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.95000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.95000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.81250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.95000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.95000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.93750 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 51.87500 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: B 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 GLY B 1 REMARK 465 SER B 2 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 B 422 O HOH B 422 7555 1.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 7R20 B 1 120 PDB 7R20 7R20 1 120 SEQRES 1 B 120 GLY SER GLU VAL GLN LEU GLN GLU SER GLY GLY GLY LEU SEQRES 2 B 120 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 B 120 SER GLY SER ILE PHE SER GLY ASN ALA MET GLY TRP TYR SEQRES 4 B 120 ARG GLN ALA PRO GLY LYS GLN ARG GLU VAL VAL ALA VAL SEQRES 5 B 120 ILE SER ALA GLY ASN SER SER ASN TYR VAL ASP SER VAL SEQRES 6 B 120 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 120 THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 B 120 THR ALA VAL TYR TYR CYS ASN VAL VAL LYS ARG GLY PRO SEQRES 9 B 120 GLN TRP GLY MET GLU TRP GLY LYS GLY THR LEU VAL THR SEQRES 10 B 120 VAL SER SER HET GOL B 301 14 HET GOL B 302 13 HET GOL B 303 13 HET SO4 B 304 5 HET SO4 B 305 5 HET SO4 B 306 5 HET SO4 B 307 5 HET GOL B 308 14 HET GOL B 309 14 HET GOL B 310 14 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 6(C3 H8 O3) FORMUL 5 SO4 4(O4 S 2-) FORMUL 12 HOH *47(H2 O) HELIX 1 AA1 SER B 27 SER B 32 1 6 HELIX 2 AA2 ASP B 63 LYS B 66 5 4 HELIX 3 AA3 LYS B 88 THR B 92 5 5 SHEET 1 AA1 4 LEU B 6 SER B 9 0 SHEET 2 AA1 4 LEU B 20 ALA B 26 -1 O SER B 23 N SER B 9 SHEET 3 AA1 4 THR B 79 MET B 84 -1 O MET B 84 N LEU B 20 SHEET 4 AA1 4 PHE B 69 ASP B 74 -1 N THR B 70 O GLN B 83 SHEET 1 AA2 6 LEU B 13 GLN B 15 0 SHEET 2 AA2 6 THR B 114 SER B 119 1 O SER B 119 N VAL B 14 SHEET 3 AA2 6 ALA B 93 VAL B 99 -1 N TYR B 95 O THR B 114 SHEET 4 AA2 6 MET B 36 GLN B 41 -1 N TYR B 39 O TYR B 96 SHEET 5 AA2 6 GLU B 48 ILE B 53 -1 O VAL B 50 N TRP B 38 SHEET 6 AA2 6 SER B 59 TYR B 61 -1 O ASN B 60 N VAL B 52 SSBOND 1 CYS B 24 CYS B 97 1555 1555 2.05 CRYST1 45.900 45.900 103.750 90.00 90.00 90.00 P 43 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 0.021786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009639 0.00000