HEADER DE NOVO PROTEIN 24-AUG-18 6AIS TITLE LOOP DELETION MUTANT (DELETING TWO RESIDUES) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER SURFACE PROTEIN A; COMPND 3 CHAIN: O; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIA BURGDORFERI; SOURCE 3 ORGANISM_TAXID: 139; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) KEYWDS OUTER SURFACE PROTEIN A, OSPA, LIPID BINDING PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SHIGA,K.MAKABE REVDAT 3 22-NOV-23 6AIS 1 REMARK REVDAT 2 16-OCT-19 6AIS 1 JRNL REVDAT 1 03-JUL-19 6AIS 0 JRNL AUTH S.SHIGA,M.YAMANAKA,W.FUJIWARA,S.HIROTA,S.GODA,K.MAKABE JRNL TITL DOMAIN-SWAPPING DESIGN BY POLYPROLINE ROD INSERTION. JRNL REF CHEMBIOCHEM V. 20 2454 2019 JRNL REFN ESSN 1439-7633 JRNL PMID 31094059 JRNL DOI 10.1002/CBIC.201900179 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 56973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2801 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 19.7838 - 3.5224 1.00 2786 155 0.1709 0.1982 REMARK 3 2 3.5224 - 2.7984 1.00 2724 156 0.1763 0.2166 REMARK 3 3 2.7984 - 2.4454 1.00 2742 143 0.1782 0.2023 REMARK 3 4 2.4454 - 2.2221 1.00 2734 123 0.1711 0.1848 REMARK 3 5 2.2221 - 2.0630 1.00 2704 139 0.1585 0.1589 REMARK 3 6 2.0630 - 1.9415 1.00 2730 133 0.1572 0.1895 REMARK 3 7 1.9415 - 1.8444 1.00 2717 133 0.1670 0.1899 REMARK 3 8 1.8444 - 1.7641 1.00 2756 125 0.1711 0.1765 REMARK 3 9 1.7641 - 1.6962 1.00 2721 128 0.1727 0.2117 REMARK 3 10 1.6962 - 1.6377 1.00 2695 155 0.1737 0.2131 REMARK 3 11 1.6377 - 1.5866 1.00 2696 139 0.1775 0.2233 REMARK 3 12 1.5866 - 1.5412 1.00 2711 140 0.1828 0.2171 REMARK 3 13 1.5412 - 1.5007 1.00 2708 124 0.1784 0.2226 REMARK 3 14 1.5007 - 1.4641 1.00 2720 145 0.1897 0.2273 REMARK 3 15 1.4641 - 1.4308 1.00 2636 155 0.1896 0.2132 REMARK 3 16 1.4308 - 1.4004 0.99 2712 138 0.1952 0.2094 REMARK 3 17 1.4004 - 1.3723 0.99 2657 149 0.2038 0.2258 REMARK 3 18 1.3723 - 1.3465 0.99 2701 141 0.2082 0.2200 REMARK 3 19 1.3465 - 1.3224 0.99 2630 134 0.2190 0.2510 REMARK 3 20 1.3224 - 1.3000 0.99 2692 146 0.2366 0.2667 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.880 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 : 0.005 1974 REMARK 3 ANGLE : 0.793 2692 REMARK 3 CHIRALITY : 0.085 340 REMARK 3 PLANARITY : 0.004 345 REMARK 3 DIHEDRAL : 3.154 1134 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 6AIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300008852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2G8C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% W/V PEG400, 0.1 M IMIDAZOLE, PH REMARK 280 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.43800 REMARK 290 SMTRY3 2 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 APPLY THE FOLLOWING TO CHAINS: O 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 O 23 REMARK 465 SER O 24 REMARK 465 HIS O 25 REMARK 465 MET O 26 REMARK 465 LYS O 27 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 ASP O 59 -115.41 55.13 REMARK 500 ALA O 60 -12.66 78.00 REMARK 500 ALA O 83 -6.10 82.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 6AIS O 23 271 PDB 6AIS 6AIS 23 271 SEQRES 1 O 249 GLY SER HIS MET LYS ASN SER VAL SER VAL ASP LEU PRO SEQRES 2 O 249 GLY SER MET LYS VAL LEU VAL SER LYS SER SER ASN ALA SEQRES 3 O 249 ASP GLY LYS TYR ASP LEU ILE ALA THR VAL ASP ALA LEU SEQRES 4 O 249 GLU LEU SER GLY THR SER ASP LYS ASN ASN GLY SER GLY SEQRES 5 O 249 VAL LEU GLU GLY VAL LYS ALA ASP ALA SER LYS VAL LYS SEQRES 6 O 249 LEU THR ILE SER ASP ASP LEU GLY GLN THR THR LEU GLU SEQRES 7 O 249 VAL PHE LYS SER ASP GLY SER THR LEU VAL SER LYS LYS SEQRES 8 O 249 VAL THR SER LYS ASP LYS SER SER THR GLU GLU LYS PHE SEQRES 9 O 249 ASN GLU LYS GLY GLU VAL SER GLU LYS ILE ILE THR ARG SEQRES 10 O 249 ALA ASP GLY THR ARG LEU GLU TYR THR GLY ILE LYS SER SEQRES 11 O 249 ASP GLY SER GLY LYS ALA LYS GLU VAL LEU LYS GLY TYR SEQRES 12 O 249 VAL LEU GLU GLY THR LEU THR ALA GLU LYS THR THR LEU SEQRES 13 O 249 VAL VAL LYS GLU GLY THR VAL THR LEU SER LYS ASN ILE SEQRES 14 O 249 SER LYS SER GLY ALA VAL SER VAL GLU LEU ASN ASP THR SEQRES 15 O 249 ASP SER SER THR LYS LYS THR ALA ALA TRP ASN SER GLY SEQRES 16 O 249 THR SER THR LEU THR ILE THR VAL ASN SER LYS LYS THR SEQRES 17 O 249 LYS ASP LEU VAL PHE THR SER SER ASN THR ILE THR VAL SEQRES 18 O 249 GLN GLN TYR ASP SER ASN GLY THR SER LEU GLU GLY SER SEQRES 19 O 249 ALA VAL GLU ILE THR LYS LEU ASP GLU ILE LYS ASN ALA SEQRES 20 O 249 LEU LYS FORMUL 2 HOH *348(H2 O) HELIX 1 AA1 ASP O 205 THR O 208 5 4 HELIX 2 AA2 LYS O 262 LEU O 270 1 9 SHEET 1 AA1 4 VAL O 30 LEU O 34 0 SHEET 2 AA1 4 MET O 38 VAL O 42 -1 O MET O 38 N LEU O 34 SHEET 3 AA1 4 TYR O 52 VAL O 58 -1 O ILE O 55 N LEU O 41 SHEET 4 AA1 4 LEU O 61 SER O 67 -1 O LEU O 63 N ALA O 56 SHEET 1 AA212 GLY O 74 VAL O 79 0 SHEET 2 AA212 LYS O 85 ILE O 90 -1 O ILE O 90 N GLY O 74 SHEET 3 AA212 THR O 97 PHE O 102 -1 O GLU O 100 N LYS O 87 SHEET 4 AA212 LEU O 109 THR O 115 -1 O VAL O 110 N VAL O 101 SHEET 5 AA212 SER O 121 PHE O 126 -1 O GLU O 124 N LYS O 112 SHEET 6 AA212 VAL O 132 THR O 138 -1 O SER O 133 N LYS O 125 SHEET 7 AA212 ARG O 144 THR O 148 -1 O LEU O 145 N ILE O 137 SHEET 8 AA212 GLY O 156 VAL O 161 -1 O LYS O 159 N GLU O 146 SHEET 9 AA212 VAL O 166 LEU O 171 -1 O LEU O 167 N GLU O 160 SHEET 10 AA212 LYS O 175 GLU O 182 -1 O VAL O 179 N GLU O 168 SHEET 11 AA212 VAL O 185 SER O 192 -1 O LEU O 187 N VAL O 180 SHEET 12 AA212 VAL O 197 ASP O 203 -1 O SER O 198 N ASN O 190 SHEET 1 AA3 5 LYS O 210 ASN O 215 0 SHEET 2 AA3 5 THR O 220 VAL O 225 -1 O THR O 224 N THR O 211 SHEET 3 AA3 5 LYS O 228 PHE O 235 -1 O THR O 230 N ILE O 223 SHEET 4 AA3 5 ILE O 241 GLN O 245 -1 O GLN O 244 N ASP O 232 SHEET 5 AA3 5 VAL O 258 GLU O 259 -1 O VAL O 258 N VAL O 243 CRYST1 33.003 54.876 66.190 90.00 100.54 90.00 P 1 21 1 2 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 0.030300 0.000000 0.005637 0.00000 SCALE2 0.000000 0.018223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015367 0.00000