HEADER DE NOVO PROTEIN 20-NOV-17 6F0S TITLE CRYSTAL STRUCTURE OF PIZZA6-SYW COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIZZA6-SYW; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARTIFICIAL PROTEIN, BETA PROPELLER, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.NOGUCHI,E.DE ZITTER,L.VAN MEERVELT,A.R.D.VOET REVDAT 1 21-MAR-18 6F0S 0 JRNL AUTH H.NOGUCHI,B.MYLEMANS,E.DE ZITTER,L.VAN MEERVELT,J.R.H.TAME, JRNL AUTH 2 A.VOET JRNL TITL DESIGN OF TRYPTOPHAN-CONTAINING MUTANTS OF THE SYMMETRICAL JRNL TITL 2 PIZZA PROTEIN FOR BIOPHYSICAL STUDIES. JRNL REF BIOCHEM. BIOPHYS. RES. V. 497 1038 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29481797 JRNL DOI 10.1016/J.BBRC.2018.02.168 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 33026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1566 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 32.2045 - 3.3349 1.00 2888 185 0.1366 0.1474 REMARK 3 2 3.3349 - 2.6474 0.99 2855 165 0.1733 0.2067 REMARK 3 3 2.6474 - 2.3129 0.98 2859 118 0.1776 0.2117 REMARK 3 4 2.3129 - 2.1014 0.99 2873 126 0.1802 0.2243 REMARK 3 5 2.1014 - 1.9508 1.00 2861 156 0.1770 0.2206 REMARK 3 6 1.9508 - 1.8358 0.99 2866 145 0.1908 0.2184 REMARK 3 7 1.8358 - 1.7439 0.99 2843 124 0.2073 0.2785 REMARK 3 8 1.7439 - 1.6680 0.99 2874 127 0.2106 0.2114 REMARK 3 9 1.6680 - 1.6038 0.99 2840 131 0.2147 0.2871 REMARK 3 10 1.6038 - 1.5484 0.99 2854 143 0.2116 0.2727 REMARK 3 11 1.5484 - 1.5000 0.99 2847 146 0.2214 0.3075 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.840 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 : 0.008 2024 REMARK 3 ANGLE : 0.994 2833 REMARK 3 CHIRALITY : 0.064 363 REMARK 3 PLANARITY : 0.007 381 REMARK 3 DIHEDRAL : 2.968 1492 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 6F0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007527. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-16 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 : ELETTRA REMARK 200 BEAMLINE : 5.2R 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 PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.32800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM CHLORIDE, 15% (W/V) REMARK 280 PEG6000, AND 0.1 M SODIUM ACETATE PH 5.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291.15K 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 34.95500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLY A 252 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 SER A 16 O HOH A 301 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 8 46.69 -84.93 REMARK 500 THR A 14 52.32 36.29 REMARK 500 SER A 16 -86.93 -120.54 REMARK 500 PRO A 50 40.38 -82.69 REMARK 500 THR A 56 57.97 37.94 REMARK 500 SER A 58 -83.29 -116.45 REMARK 500 SER A 58 -64.59 -121.01 REMARK 500 PRO A 92 42.84 -81.26 REMARK 500 THR A 98 56.68 38.71 REMARK 500 SER A 100 -92.67 -118.13 REMARK 500 SER A 100 -89.47 -119.70 REMARK 500 PRO A 134 48.19 -82.21 REMARK 500 THR A 140 53.62 37.81 REMARK 500 SER A 142 -61.59 -126.63 REMARK 500 SER A 142 -84.38 -120.99 REMARK 500 PRO A 176 49.19 -80.47 REMARK 500 SER A 184 -74.83 -122.74 REMARK 500 SER A 184 -76.70 -121.35 REMARK 500 PRO A 218 43.00 -82.97 REMARK 500 THR A 224 57.02 38.61 REMARK 500 SER A 226 -90.54 -125.70 REMARK 500 SER A 226 -85.83 -130.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 6F0S A -3 252 PDB 6F0S 6F0S -3 252 SEQRES 1 A 256 GLY SER HIS MET SER ASN THR GLN THR VAL LEU PRO PHE SEQRES 2 A 256 THR GLY LEU ASN THR PRO SER GLY VAL ALA VAL ASP SER SEQRES 3 A 256 ALA GLY THR VAL TRP VAL THR ASP HIS GLY ASN ASN ARG SEQRES 4 A 256 VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR VAL SEQRES 5 A 256 LEU PRO PHE THR GLY LEU ASN THR PRO SER GLY VAL ALA SEQRES 6 A 256 VAL ASP SER ALA GLY THR VAL TYR VAL THR ASP HIS GLY SEQRES 7 A 256 ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR SEQRES 8 A 256 GLN THR VAL LEU PRO PHE THR GLY LEU ASN THR PRO SER SEQRES 9 A 256 GLY VAL ALA VAL ASP SER ALA GLY THR VAL TRP VAL THR SEQRES 10 A 256 ASP HIS GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SEQRES 11 A 256 SER ASN THR GLN THR VAL LEU PRO PHE THR GLY LEU ASN SEQRES 12 A 256 THR PRO SER GLY VAL ALA VAL ASP SER ALA GLY THR VAL SEQRES 13 A 256 TYR VAL THR ASP HIS GLY ASN ASN ARG VAL VAL LYS LEU SEQRES 14 A 256 ALA ALA GLY SER ASN THR GLN THR VAL LEU PRO PHE THR SEQRES 15 A 256 GLY LEU ASN THR PRO SER GLY VAL ALA VAL ASP SER ALA SEQRES 16 A 256 GLY THR VAL TRP VAL THR ASP HIS GLY ASN ASN ARG VAL SEQRES 17 A 256 VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR VAL LEU SEQRES 18 A 256 PRO PHE THR GLY LEU ASN THR PRO SER GLY VAL ALA VAL SEQRES 19 A 256 ASP SER ALA GLY THR VAL TYR VAL THR ASP HIS GLY ASN SEQRES 20 A 256 ASN ARG VAL VAL LYS LEU ALA ALA GLY FORMUL 2 HOH *247(H2 O) HELIX 1 AA1 HIS A 31 ASN A 34 5 4 HELIX 2 AA2 HIS A 73 ASN A 76 5 4 HELIX 3 AA3 HIS A 115 ASN A 118 5 4 HELIX 4 AA4 HIS A 157 ASN A 160 5 4 HELIX 5 AA5 HIS A 199 ASN A 202 5 4 HELIX 6 AA6 HIS A 241 ASN A 244 5 4 SHEET 1 AA1 4 THR A 5 VAL A 6 0 SHEET 2 AA1 4 ARG A 245 LEU A 249 -1 O LYS A 248 N THR A 5 SHEET 3 AA1 4 VAL A 236 ASP A 240 -1 N VAL A 238 O VAL A 247 SHEET 4 AA1 4 VAL A 228 VAL A 230 -1 N ALA A 229 O TYR A 237 SHEET 1 AA2 4 VAL A 18 VAL A 20 0 SHEET 2 AA2 4 VAL A 26 ASP A 30 -1 O TRP A 27 N ALA A 19 SHEET 3 AA2 4 ARG A 35 LEU A 39 -1 O LEU A 39 N VAL A 26 SHEET 4 AA2 4 THR A 47 VAL A 48 -1 O THR A 47 N LYS A 38 SHEET 1 AA3 4 VAL A 60 VAL A 62 0 SHEET 2 AA3 4 VAL A 68 ASP A 72 -1 O TYR A 69 N ALA A 61 SHEET 3 AA3 4 ARG A 77 LEU A 81 -1 O VAL A 79 N VAL A 70 SHEET 4 AA3 4 GLN A 88 VAL A 90 -1 O THR A 89 N LYS A 80 SHEET 1 AA4 4 VAL A 102 VAL A 104 0 SHEET 2 AA4 4 VAL A 110 ASP A 114 -1 O TRP A 111 N ALA A 103 SHEET 3 AA4 4 ARG A 119 LEU A 123 -1 O VAL A 121 N VAL A 112 SHEET 4 AA4 4 GLN A 130 VAL A 132 -1 O THR A 131 N LYS A 122 SHEET 1 AA5 4 VAL A 144 VAL A 146 0 SHEET 2 AA5 4 VAL A 152 ASP A 156 -1 O TYR A 153 N ALA A 145 SHEET 3 AA5 4 ARG A 161 LEU A 165 -1 O VAL A 163 N VAL A 154 SHEET 4 AA5 4 GLN A 172 VAL A 174 -1 O THR A 173 N LYS A 164 SHEET 1 AA6 4 VAL A 186 VAL A 188 0 SHEET 2 AA6 4 VAL A 194 ASP A 198 -1 O TRP A 195 N ALA A 187 SHEET 3 AA6 4 ARG A 203 LEU A 207 -1 O VAL A 205 N VAL A 196 SHEET 4 AA6 4 THR A 215 VAL A 216 -1 O THR A 215 N LYS A 206 CRYST1 33.710 69.910 46.940 90.00 107.23 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 0.029665 0.000000 0.009200 0.00000 SCALE2 0.000000 0.014304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022305 0.00000