HEADER IMMUNE SYSTEM 17-AUG-17 6APO TITLE ANTI-MARBURGVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-MARBURGVIRUS NUCLEOPROTEIN SINGLE DOMAIN ANTIBODY A; 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 SINGLE DOMAIN ANTIBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.B.TAYLOR,J.A.GARZA REVDAT 3 04-OCT-23 6APO 1 REMARK REVDAT 2 16-MAY-18 6APO 1 JRNL REVDAT 1 11-OCT-17 6APO 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. 1.17 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 39980 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 37.8100 - 2.8143 0.99 2992 158 0.1621 0.2018 REMARK 3 2 2.8143 - 2.2339 1.00 2898 152 0.1724 0.1844 REMARK 3 3 2.2339 - 1.9515 1.00 2860 151 0.1477 0.1669 REMARK 3 4 1.9515 - 1.7731 1.00 2847 150 0.1401 0.1512 REMARK 3 5 1.7731 - 1.6460 1.00 2829 149 0.1360 0.1823 REMARK 3 6 1.6460 - 1.5490 1.00 2826 149 0.1256 0.1364 REMARK 3 7 1.5490 - 1.4714 1.00 2811 148 0.1230 0.1435 REMARK 3 8 1.4714 - 1.4073 1.00 2815 148 0.1199 0.1423 REMARK 3 9 1.4073 - 1.3532 1.00 2822 149 0.1221 0.1495 REMARK 3 10 1.3532 - 1.3065 1.00 2775 146 0.1249 0.1389 REMARK 3 11 1.3065 - 1.2656 1.00 2786 146 0.1265 0.1550 REMARK 3 12 1.2656 - 1.2294 1.00 2798 148 0.1371 0.1667 REMARK 3 13 1.2294 - 1.1971 0.87 2415 126 0.1586 0.1856 REMARK 3 14 1.1971 - 1.1680 0.54 1506 80 0.1777 0.2190 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.80 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 : 0.007 980 REMARK 3 ANGLE : 0.967 1341 REMARK 3 CHIRALITY : 0.086 145 REMARK 3 PLANARITY : 0.008 173 REMARK 3 DIHEDRAL : 13.887 369 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 6APO 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_1000229567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-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 : 40045 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.168 REMARK 200 RESOLUTION RANGE LOW (A) : 41.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28200 REMARK 200 FOR SHELL : 3.400 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: 1YC7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% POLYETHYLENE GLYCOL 1000, 0.1M REMARK 280 TRIS-HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 20.79850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.40700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.68100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.40700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.79850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.68100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 GLU A 1 REMARK 465 VAL A 2 REMARK 465 GLY A 119 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 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 205 O HOH A 304 2.08 REMARK 500 O HOH A 292 O HOH A 324 2.15 REMARK 500 O HOH A 338 O HOH A 369 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6APO A 1 126 PDB 6APO 6APO 1 126 SEQRES 1 A 126 GLU VAL LYS LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 126 ALA GLY GLU SER LEU ARG LEU SER CYS ALA VAL PRO PRO SEQRES 3 A 126 GLU VAL PHE ASP ILE ARG THR VAL ALA TRP TYR ARG GLN SEQRES 4 A 126 VAL PRO LEU GLY LYS GLY ARG GLU LEU LEU SER SER ILE SEQRES 5 A 126 THR PRO TRP ASN LYS THR THR TYR GLU ASP SER VAL LYS SEQRES 6 A 126 ASP ARG PHE THR ILE SER ARG ASP ASN ALA LYS TYR THR SEQRES 7 A 126 VAL TYR LEU GLN MET ASN ASP LEU LYS PRO GLU ASP THR SEQRES 8 A 126 ALA VAL TYR TYR CYS ALA GLN GLY TRP GLY ILE ALA SER SEQRES 9 A 126 MET ARG TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 A 126 SER GLY GLY HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *176(H2 O) HELIX 1 AA1 PRO A 25 ASP A 30 1 6 HELIX 2 AA2 ASP A 62 LYS A 65 5 4 HELIX 3 AA3 LYS A 87 THR A 91 5 5 HELIX 4 AA4 GLY A 101 ALA A 103 5 3 SHEET 1 AA1 4 GLN A 5 SER A 7 0 SHEET 2 AA1 4 LEU A 18 ALA A 23 -1 O ALA A 23 N GLN A 5 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O LEU A 81 N LEU A 20 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N THR A 69 O GLN A 82 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 92 GLY A 99 -1 N TYR A 94 O THR A 112 SHEET 4 AA2 6 THR A 33 GLN A 39 -1 N TYR A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 47 ILE A 52 -1 O GLU A 47 N ARG A 38 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O THR A 59 N SER A 51 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 92 GLY A 99 -1 N TYR A 94 O THR A 112 SHEET 4 AA3 4 MET A 105 TRP A 108 -1 O TYR A 107 N GLN A 98 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.07 CRYST1 41.597 49.362 58.814 90.00 90.00 90.00 P 21 21 21 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 0.024040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017003 0.00000