HEADER IMMUNE SYSTEM 17-AUG-17 6APQ TITLE ANTI-MARBURGVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-MARBURGVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY B; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES 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; SOURCE 8 OTHER_DETAILS: SEMI-SYNTHETIC SINGLE POT LIBRARY NOMAD 1 BASED UPON SOURCE 9 LAMA GLAMA KEYWDS IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.B.TAYLOR,J.A.GARZA REVDAT 3 04-OCT-23 6APQ 1 REMARK REVDAT 2 16-MAY-18 6APQ 1 JRNL REVDAT 1 11-OCT-17 6APQ 0 JRNL AUTH J.A.GARZA,A.B.TAYLOR,L.J.SHERWOOD,P.J.HART,A.HAYHURST JRNL TITL UNVEILING A DRIFT RESISTANT CRYPTOTOPE JRNL TITL 2 WITHINMARBURGVIRUSNUCLEOPROTEIN RECOGNIZED BY LLAMA JRNL TITL 3 SINGLE-DOMAIN ANTIBODIES. JRNL REF FRONT IMMUNOL V. 8 1234 2017 JRNL REFN ESSN 1664-3224 JRNL PMID 29038656 JRNL DOI 10.3389/FIMMU.2017.01234 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13899 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1390 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 69.3177 - 4.0932 0.99 1364 152 0.1741 0.1962 REMARK 3 2 4.0932 - 3.2489 1.00 1286 144 0.1579 0.1646 REMARK 3 3 3.2489 - 2.8382 1.00 1258 139 0.1878 0.2174 REMARK 3 4 2.8382 - 2.5787 1.00 1241 138 0.1894 0.2412 REMARK 3 5 2.5787 - 2.3939 1.00 1243 137 0.2036 0.2450 REMARK 3 6 2.3939 - 2.2527 1.00 1236 137 0.2067 0.2827 REMARK 3 7 2.2527 - 2.1399 1.00 1230 137 0.1806 0.2381 REMARK 3 8 2.1399 - 2.0467 1.00 1220 136 0.2036 0.2538 REMARK 3 9 2.0467 - 1.9679 1.00 1215 135 0.2275 0.2691 REMARK 3 10 1.9679 - 1.9000 1.00 1216 135 0.2465 0.2856 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90 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 : 0.007 922 REMARK 3 ANGLE : 1.103 1243 REMARK 3 CHIRALITY : 0.053 129 REMARK 3 PLANARITY : 0.004 161 REMARK 3 DIHEDRAL : 18.824 333 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 6APQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-10 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97917 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13942 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 69.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58700 REMARK 200 FOR SHELL : 2.500 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: 6APO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.0M SODIUM CHLORIDE, 0.1M BICINE PH REMARK 280 9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 59.92933 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 29.96467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.94700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.98233 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 74.91167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.92933 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 29.96467 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 14.98233 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 44.94700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 74.91167 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 344 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 427 LIES ON A SPECIAL POSITION. 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 A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 73 O REMARK 620 2 ASN A 76 OD1 91.2 REMARK 620 3 HOH A 369 O 82.6 93.8 REMARK 620 4 HOH A 372 O 106.8 104.2 159.3 REMARK 620 5 HOH A 373 O 154.2 78.9 74.4 98.8 REMARK 620 6 HOH A 414 O 153.0 84.6 124.2 49.3 50.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 204 DBREF 6APQ A 1 126 PDB 6APQ 6APQ 1 126 SEQRES 1 A 126 LYS VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 126 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 126 GLY THR PHE SER ILE ASN THR LEU GLY TRP TYR ARG ARG SEQRES 4 A 126 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ARG ILE SER SEQRES 5 A 126 SER GLY GLY ILE THR ARG TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 126 ARG PHE THR ILE SER ARG ASP ASN GLY LYS ASN THR VAL SEQRES 7 A 126 TYR LEU ASP MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 A 126 VAL TYR TYR CYS MET TYR ARG ASN TRP GLY GLY GLY LEU SEQRES 9 A 126 ASP VAL TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 A 126 SER GLY GLY HIS HIS HIS HIS HIS HIS HET NA A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 CL 3(CL 1-) FORMUL 6 HOH *135(H2 O) HELIX 1 AA1 THR A 28 ASN A 32 5 5 HELIX 2 AA2 ASN A 73 LYS A 75 5 3 HELIX 3 AA3 LYS A 86 THR A 90 5 5 SHEET 1 AA1 4 GLN A 3 GLY A 8 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 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 112 SER A 117 1 O SER A 117 N VAL A 12 SHEET 3 AA2 6 ALA A 91 ARG A 98 -1 N TYR A 93 O THR A 112 SHEET 4 AA2 6 THR A 33 ARG A 39 -1 N THR A 33 O ARG A 98 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O ARG A 58 N ARG A 50 SHEET 1 AA3 4 GLY A 10 GLN A 13 0 SHEET 2 AA3 4 THR A 112 SER A 117 1 O SER A 117 N VAL A 12 SHEET 3 AA3 4 ALA A 91 ARG A 98 -1 N TYR A 93 O THR A 112 SHEET 4 AA3 4 VAL A 106 TRP A 108 -1 O TYR A 107 N TYR A 97 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.05 LINK O ASN A 73 NA NA A 201 1555 1555 2.24 LINK OD1 ASN A 76 NA NA A 201 1555 1555 2.34 LINK NA NA A 201 O HOH A 369 1555 1555 2.20 LINK NA NA A 201 O HOH A 372 1555 1555 2.32 LINK NA NA A 201 O HOH A 373 1555 1555 2.41 LINK NA NA A 201 O HOH A 414 1555 1555 3.18 SITE 1 AC1 5 ASN A 73 ASN A 76 HOH A 369 HOH A 372 SITE 2 AC1 5 HOH A 373 SITE 1 AC2 3 GLY A 27 ASN A 76 TYR A 97 SITE 1 AC3 2 TYR A 59 LYS A 64 SITE 1 AC4 4 TYR A 37 ARG A 50 MET A 96 ARG A 98 CRYST1 79.988 79.988 89.894 90.00 90.00 120.00 P 65 2 2 12 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 0.012502 0.007218 0.000000 0.00000 SCALE2 0.000000 0.014436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011124 0.00000