HEADER DE NOVO PROTEIN 09-SEP-18 6IDC TITLE LOOP DELETION AND PROLINE INSERTION MUTANT (DELETING SIX RESIDUES AND TITLE 2 INSERTED SIX PROLINE RESIDUES) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER SURFACE PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIA BURGDORFERI; SOURCE 3 ORGANISM_TAXID: 139; SOURCE 4 GENE: OSPA, BB_A15; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) KEYWDS OUTER SURFACE PROTEIN A, LIPID BINDING PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SHIGA,K.MAKABE REVDAT 3 22-NOV-23 6IDC 1 REMARK REVDAT 2 16-OCT-19 6IDC 1 JRNL REVDAT 1 03-JUL-19 6IDC 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. 2.01 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 2034 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 19.9042 - 4.9260 1.00 2600 188 0.1952 0.1906 REMARK 3 2 4.9260 - 3.9197 1.00 2522 148 0.1593 0.1785 REMARK 3 3 3.9197 - 3.4271 1.00 2516 142 0.1890 0.2184 REMARK 3 4 3.4271 - 3.1150 1.00 2481 158 0.2291 0.2485 REMARK 3 5 3.1150 - 2.8925 1.00 2506 132 0.2410 0.2926 REMARK 3 6 2.8925 - 2.7224 1.00 2503 138 0.2517 0.2409 REMARK 3 7 2.7224 - 2.5864 1.00 2479 121 0.2508 0.3216 REMARK 3 8 2.5864 - 2.4740 1.00 2475 132 0.2576 0.2737 REMARK 3 9 2.4740 - 2.3789 1.00 2485 115 0.2433 0.2903 REMARK 3 10 2.3789 - 2.2969 1.00 2489 118 0.2461 0.2950 REMARK 3 11 2.2969 - 2.2252 1.00 2489 118 0.2410 0.2807 REMARK 3 12 2.2252 - 2.1617 1.00 2467 119 0.2391 0.2760 REMARK 3 13 2.1617 - 2.1048 1.00 2472 123 0.2375 0.2397 REMARK 3 14 2.1048 - 2.0535 1.00 2495 131 0.2554 0.2966 REMARK 3 15 2.0535 - 2.0069 0.98 2356 151 0.2524 0.3018 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.550 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 : 0.007 1868 REMARK 3 ANGLE : 0.820 2521 REMARK 3 CHIRALITY : 0.055 314 REMARK 3 PLANARITY : 0.005 317 REMARK 3 DIHEDRAL : 2.908 1163 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: THE AUTHORS SCALED THE SAMPLE DATA AS REMARK 3 P3, BUT REFINED THE DATA AS P321. REMARK 4 REMARK 4 6IDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300009009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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-5A 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 PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75395 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.150 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 (%): 77.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 34.09633 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 68.19267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.19267 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 34.09633 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 68.19267 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 SER A 107 -23.36 -141.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 6IDC A 27 273 UNP P0CL66 OSPA_BORBU 27 273 SEQADV 6IDC GLY A 23 UNP P0CL66 EXPRESSION TAG SEQADV 6IDC SER A 24 UNP P0CL66 EXPRESSION TAG SEQADV 6IDC HIS A 25 UNP P0CL66 EXPRESSION TAG SEQADV 6IDC MET A 26 UNP P0CL66 EXPRESSION TAG SEQADV 6IDC SER A 37 UNP P0CL66 GLU 37 ENGINEERED MUTATION SEQADV 6IDC SER A 45 UNP P0CL66 GLU 45 ENGINEERED MUTATION SEQADV 6IDC SER A 46 UNP P0CL66 LYS 46 ENGINEERED MUTATION SEQADV 6IDC ALA A 48 UNP P0CL66 LYS 48 ENGINEERED MUTATION SEQADV 6IDC ALA A 60 UNP P0CL66 LYS 60 ENGINEERED MUTATION SEQADV 6IDC SER A 64 UNP P0CL66 LYS 64 ENGINEERED MUTATION SEQADV 6IDC ALA A 83 UNP P0CL66 LYS 83 ENGINEERED MUTATION SEQADV 6IDC SER A 104 UNP P0CL66 GLU 104 ENGINEERED MUTATION SEQADV 6IDC SER A 107 UNP P0CL66 LYS 107 ENGINEERED MUTATION SEQADV 6IDC ALA A 196 UNP P0CL66 GLU 196 ENGINEERED MUTATION SEQADV 6IDC PRO A 205 UNP P0CL66 ASP 205 ENGINEERED MUTATION SEQADV 6IDC PRO A 206 UNP P0CL66 SER 206 ENGINEERED MUTATION SEQADV 6IDC PRO A 207 UNP P0CL66 SER 207 ENGINEERED MUTATION SEQADV 6IDC PRO A 208 UNP P0CL66 ALA 208 ENGINEERED MUTATION SEQADV 6IDC PRO A 209 UNP P0CL66 ALA 209 ENGINEERED MUTATION SEQADV 6IDC PRO A 210 UNP P0CL66 THR 210 ENGINEERED MUTATION SEQADV 6IDC SER A 239 UNP P0CL66 LYS 239 ENGINEERED MUTATION SEQADV 6IDC SER A 240 UNP P0CL66 GLU 240 ENGINEERED MUTATION SEQADV 6IDC SER A 254 UNP P0CL66 LYS 254 ENGINEERED MUTATION SEQRES 1 A 251 GLY SER HIS MET LYS ASN SER VAL SER VAL ASP LEU PRO SEQRES 2 A 251 GLY SER MET LYS VAL LEU VAL SER LYS SER SER ASN ALA SEQRES 3 A 251 ASP GLY LYS TYR ASP LEU ILE ALA THR VAL ASP ALA LEU SEQRES 4 A 251 GLU LEU SER GLY THR SER ASP LYS ASN ASN GLY SER GLY SEQRES 5 A 251 VAL LEU GLU GLY VAL LYS ALA ASP ALA SER LYS VAL LYS SEQRES 6 A 251 LEU THR ILE SER ASP ASP LEU GLY GLN THR THR LEU GLU SEQRES 7 A 251 VAL PHE LYS SER ASP GLY SER THR LEU VAL SER LYS LYS SEQRES 8 A 251 VAL THR SER LYS ASP LYS SER SER THR GLU GLU LYS PHE SEQRES 9 A 251 ASN GLU LYS GLY GLU VAL SER GLU LYS ILE ILE THR ARG SEQRES 10 A 251 ALA ASP GLY THR ARG LEU GLU TYR THR GLY ILE LYS SER SEQRES 11 A 251 ASP GLY SER GLY LYS ALA LYS GLU VAL LEU LYS GLY TYR SEQRES 12 A 251 VAL LEU GLU GLY THR LEU THR ALA GLU LYS THR THR LEU SEQRES 13 A 251 VAL VAL LYS GLU GLY THR VAL THR LEU SER LYS ASN ILE SEQRES 14 A 251 SER LYS SER GLY ALA VAL SER VAL GLU LEU ASN ASP THR SEQRES 15 A 251 PRO PRO PRO PRO PRO PRO LYS LYS THR ALA ALA TRP ASN SEQRES 16 A 251 SER GLY THR SER THR LEU THR ILE THR VAL ASN SER LYS SEQRES 17 A 251 LYS THR LYS ASP LEU VAL PHE THR SER SER ASN THR ILE SEQRES 18 A 251 THR VAL GLN GLN TYR ASP SER ASN GLY THR SER LEU GLU SEQRES 19 A 251 GLY SER ALA VAL GLU ILE THR LYS LEU ASP GLU ILE LYS SEQRES 20 A 251 ASN ALA LEU LYS FORMUL 2 HOH *182(H2 O) HELIX 1 AA1 LYS A 264 LYS A 273 1 10 SHEET 1 AA1 4 SER A 29 LEU A 34 0 SHEET 2 AA1 4 MET A 38 SER A 43 -1 O MET A 38 N LEU A 34 SHEET 3 AA1 4 TYR A 52 VAL A 58 -1 O ILE A 55 N LEU A 41 SHEET 4 AA1 4 LEU A 61 SER A 67 -1 O LEU A 63 N ALA A 56 SHEET 1 AA212 GLY A 74 VAL A 79 0 SHEET 2 AA212 LYS A 85 ILE A 90 -1 O ILE A 90 N GLY A 74 SHEET 3 AA212 GLN A 96 PHE A 102 -1 O PHE A 102 N LYS A 85 SHEET 4 AA212 LEU A 109 SER A 116 -1 O VAL A 110 N VAL A 101 SHEET 5 AA212 SER A 121 PHE A 126 -1 O THR A 122 N VAL A 114 SHEET 6 AA212 VAL A 132 THR A 138 -1 O THR A 138 N SER A 121 SHEET 7 AA212 ARG A 144 THR A 148 -1 O TYR A 147 N LYS A 135 SHEET 8 AA212 GLY A 156 VAL A 161 -1 O LYS A 159 N GLU A 146 SHEET 9 AA212 VAL A 166 LEU A 171 -1 O LEU A 171 N GLY A 156 SHEET 10 AA212 LYS A 175 GLU A 182 -1 O VAL A 179 N GLU A 168 SHEET 11 AA212 VAL A 185 SER A 192 -1 O LEU A 187 N VAL A 180 SHEET 12 AA212 VAL A 197 ASP A 203 -1 O SER A 198 N ASN A 190 SHEET 1 AA3 5 LYS A 212 ASN A 217 0 SHEET 2 AA3 5 THR A 222 VAL A 227 -1 O THR A 226 N THR A 213 SHEET 3 AA3 5 LYS A 230 PHE A 237 -1 O LEU A 235 N LEU A 223 SHEET 4 AA3 5 ILE A 243 GLN A 247 -1 O GLN A 246 N ASP A 234 SHEET 5 AA3 5 VAL A 260 GLU A 261 -1 O VAL A 260 N VAL A 245 CRYST1 99.383 99.383 102.289 90.00 90.00 120.00 P 31 2 1 6 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 0.010062 0.005809 0.000000 0.00000 SCALE2 0.000000 0.011619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009776 0.00000