HEADER LIPID BINDING PROTEIN 11-JAN-19 6J5O TITLE OSPA MUTANT, PSAM-VLGDV1-FORM5, GRAFTED SHORT CHAMELEON SEQUENCE FROM TITLE 2 ALPHA-B CRYSTALLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER SURFACE PROTEIN A; COMPND 3 CHAIN: O; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIELLA BURGDORFERI; SOURCE 3 ORGANISM_COMMON: LYME DISEASE SPIROCHETE; SOURCE 4 ORGANISM_TAXID: 139; SOURCE 5 GENE: OSPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PEPTIDE SELF-ASSEMBLY MIMIC, SINGLE-LAYER BETA-SHEET, CHAMELEON KEYWDS 2 SEQUENCE, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.FUJIWARA,K.MAKABE REVDAT 2 22-NOV-23 6J5O 1 JRNL REVDAT 1 27-NOV-19 6J5O 0 JRNL AUTH H.FUJIWARA,K.HONGO,Y.HORI,N.YOSHIDA,K.MAKABE JRNL TITL BETA-SHEET ELASTICITY OF PEPTIDE SELF-ASSEMBLY MIMIC, PSAM, JRNL TITL 2 WITH A GRAFTED SEQUENCE CHARACTERIZED BY COMPREHENSIVE JRNL TITL 3 ANALYSES OF ISOMORPHOUS CRYSTALS JRNL REF J MOL LIQ V. 290 2019 JRNL REFN ESSN 1873-3166 JRNL DOI 10.1016/J.MOLLIQ.2019.111161 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 19.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 17912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.230 REMARK 3 FREE R VALUE TEST SET COUNT : 937 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 19.7578 - 3.6273 0.99 2486 144 0.1771 0.1903 REMARK 3 2 3.6273 - 2.8820 1.00 2469 131 0.1975 0.2355 REMARK 3 3 2.8820 - 2.5185 1.00 2456 114 0.2352 0.2848 REMARK 3 4 2.5185 - 2.2886 0.99 2410 144 0.2428 0.2740 REMARK 3 5 2.2886 - 2.1248 0.99 2420 124 0.2352 0.2714 REMARK 3 6 2.1248 - 1.9996 0.99 2444 136 0.2671 0.3671 REMARK 3 7 1.9996 - 1.8996 0.95 2290 144 0.2989 0.3529 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.460 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 : 0.006 1816 REMARK 3 ANGLE : 0.761 2448 REMARK 3 CHIRALITY : 0.054 312 REMARK 3 PLANARITY : 0.003 305 REMARK 3 DIHEDRAL : 17.321 672 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 6J5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17958 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 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) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.69900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.340 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5B2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 38% PEG 400, REMARK 280 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 26.89950 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 ALA O 83 -1.44 80.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH O 483 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH O 484 DISTANCE = 8.52 ANGSTROMS REMARK 525 HOH O 485 DISTANCE = 9.29 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B2A RELATED DB: PDB DBREF 6J5O O 27 273 UNP Q45040 Q45040_BORBG 27 273 SEQADV 6J5O GLY O 23 UNP Q45040 EXPRESSION TAG SEQADV 6J5O SER O 24 UNP Q45040 EXPRESSION TAG SEQADV 6J5O HIS O 25 UNP Q45040 EXPRESSION TAG SEQADV 6J5O MET O 26 UNP Q45040 EXPRESSION TAG SEQADV 6J5O SER O 37 UNP Q45040 GLU 37 ENGINEERED MUTATION SEQADV 6J5O SER O 45 UNP Q45040 GLU 45 ENGINEERED MUTATION SEQADV 6J5O SER O 46 UNP Q45040 LYS 46 ENGINEERED MUTATION SEQADV 6J5O ALA O 48 UNP Q45040 LYS 48 ENGINEERED MUTATION SEQADV 6J5O ALA O 60 UNP Q45040 LYS 60 ENGINEERED MUTATION SEQADV 6J5O SER O 64 UNP Q45040 LYS 64 ENGINEERED MUTATION SEQADV 6J5O ALA O 83 UNP Q45040 LYS 83 ENGINEERED MUTATION SEQADV 6J5O SER O 104 UNP Q45040 GLU 104 ENGINEERED MUTATION SEQADV 6J5O SER O 107 UNP Q45040 LYS 107 ENGINEERED MUTATION SEQADV 6J5O VAL O 120 UNP Q45040 SER 120 ENGINEERED MUTATION SEQADV 6J5O LEU O 121 UNP Q45040 SER 121 ENGINEERED MUTATION SEQADV 6J5O GLY O 122 UNP Q45040 THR 122 ENGINEERED MUTATION SEQADV 6J5O ASP O 123 UNP Q45040 GLU 123 ENGINEERED MUTATION SEQADV 6J5O VAL O 124 UNP Q45040 GLU 124 ENGINEERED MUTATION SEQADV 6J5O ALA O 196 UNP Q45040 GLU 196 ENGINEERED MUTATION SEQADV 6J5O SER O 239 UNP Q45040 LYS 239 ENGINEERED MUTATION SEQADV 6J5O SER O 240 UNP Q45040 GLU 240 ENGINEERED MUTATION SEQADV 6J5O SER O 254 UNP Q45040 LYS 254 ENGINEERED MUTATION SEQRES 1 O 251 GLY SER HIS MET LYS ASN SER VAL SER VAL ASP LEU PRO SEQRES 2 O 251 GLY SER MET LYS VAL LEU VAL SER LYS SER SER ASN ALA SEQRES 3 O 251 ASP GLY LYS TYR ASP LEU ILE ALA THR VAL ASP ALA LEU SEQRES 4 O 251 GLU LEU SER GLY THR SER ASP LYS ASN ASN GLY SER GLY SEQRES 5 O 251 VAL LEU GLU GLY VAL LYS ALA ASP ALA SER LYS VAL LYS SEQRES 6 O 251 LEU THR ILE SER ASP ASP LEU GLY GLN THR THR LEU GLU SEQRES 7 O 251 VAL PHE LYS SER ASP GLY SER THR LEU VAL SER LYS LYS SEQRES 8 O 251 VAL THR SER LYS ASP LYS VAL LEU GLY ASP VAL LYS PHE SEQRES 9 O 251 ASN GLU LYS GLY GLU VAL SER GLU LYS ILE ILE THR ARG SEQRES 10 O 251 ALA ASP GLY THR ARG LEU GLU TYR THR GLY ILE LYS SER SEQRES 11 O 251 ASP GLY SER GLY LYS ALA LYS GLU VAL LEU LYS GLY TYR SEQRES 12 O 251 VAL LEU GLU GLY THR LEU THR ALA GLU LYS THR THR LEU SEQRES 13 O 251 VAL VAL LYS GLU GLY THR VAL THR LEU SER LYS ASN ILE SEQRES 14 O 251 SER LYS SER GLY ALA VAL SER VAL GLU LEU ASN ASP THR SEQRES 15 O 251 ASP SER SER ALA ALA THR LYS LYS THR ALA ALA TRP ASN SEQRES 16 O 251 SER GLY THR SER THR LEU THR ILE THR VAL ASN SER LYS SEQRES 17 O 251 LYS THR LYS ASP LEU VAL PHE THR SER SER ASN THR ILE SEQRES 18 O 251 THR VAL GLN GLN TYR ASP SER ASN GLY THR SER LEU GLU SEQRES 19 O 251 GLY SER ALA VAL GLU ILE THR LYS LEU ASP GLU ILE LYS SEQRES 20 O 251 ASN ALA LEU LYS FORMUL 2 HOH *185(H2 O) HELIX 1 AA1 LYS O 264 LEU O 272 1 9 SHEET 1 AA1 4 SER O 29 LEU O 34 0 SHEET 2 AA1 4 MET O 38 SER O 43 -1 O VAL O 42 N VAL O 30 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 SER O 67 N TYR O 52 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 THR O 98 N THR O 89 SHEET 4 AA212 LEU O 109 THR O 115 -1 O VAL O 110 N VAL O 101 SHEET 5 AA212 LEU O 121 PHE O 126 -1 O GLY O 122 N VAL O 114 SHEET 6 AA212 VAL O 132 THR O 138 -1 O THR O 138 N LEU O 121 SHEET 7 AA212 ARG O 144 THR O 148 -1 O TYR O 147 N LYS O 135 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 171 N GLY O 156 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 212 ASN O 217 0 SHEET 2 AA3 5 THR O 222 VAL O 227 -1 O THR O 224 N ALA O 215 SHEET 3 AA3 5 LYS O 230 PHE O 237 -1 O LYS O 230 N VAL O 227 SHEET 4 AA3 5 ILE O 243 GLN O 247 -1 O GLN O 246 N ASP O 234 SHEET 5 AA3 5 VAL O 260 GLU O 261 -1 O VAL O 260 N VAL O 245 CRYST1 33.121 53.799 65.925 90.00 99.99 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 0.030192 0.000000 0.005318 0.00000 SCALE2 0.000000 0.018588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015402 0.00000