HEADER DE NOVO PROTEIN 17-JUN-14 3WWA TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED PIZZA7 PROTEIN AFTER TITLE 2 HEAT TREATMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIZZA7H PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS DESIGNED. KEYWDS COMPUTATIONAL PROTEIN DESIGN, SELF-ASSEMBLY, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.D.VOET,H.NOGUCHI,C.ADDY,D.SIMONCINI,D.TERADA,S.UNZAI,S.Y.PARK, AUTHOR 2 K.Y.J.ZHANG,J.R.H.TAME REVDAT 3 20-MAR-24 3WWA 1 REMARK REVDAT 2 05-NOV-14 3WWA 1 JRNL REVDAT 1 08-OCT-14 3WWA 0 JRNL AUTH A.R.D.VOET,H.NOGUCHI,C.ADDY,D.SIMONCINI,D.TERADA,S.UNZAI, JRNL AUTH 2 S.Y.PARK,K.Y.J.ZHANG,J.R.H.TAME JRNL TITL COMPUTATIONAL DESIGN OF A SELF-ASSEMBLING SYMMETRICAL JRNL TITL 2 BETA-PROPELLER PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 15102 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 25288768 JRNL DOI 10.1073/PNAS.1412768111 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1412) 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 17919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 910 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 34.7096 - 3.6115 0.92 2767 179 0.1648 0.2266 REMARK 3 2 3.6115 - 2.8670 0.99 2881 152 0.1817 0.2561 REMARK 3 3 2.8670 - 2.5047 1.00 2896 133 0.2180 0.2790 REMARK 3 4 2.5047 - 2.2758 1.00 2905 149 0.2222 0.3162 REMARK 3 5 2.2758 - 2.1127 1.00 2803 162 0.2262 0.2804 REMARK 3 6 2.1127 - 1.9881 0.96 2757 135 0.2332 0.3011 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 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 1822 REMARK 3 ANGLE : 1.223 2509 REMARK 3 CHIRALITY : 0.084 318 REMARK 3 PLANARITY : 0.005 334 REMARK 3 DIHEDRAL : 8.758 610 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 3WWA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000096872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 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) : 1.988 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.2700 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.690 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085M HEPES SODIUM SALT PH 7.5, 8.5% REMARK 280 ISOPROPANOL, 17% PEG 4000, 15% GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 20.02800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.15050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.74900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.15050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.02800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.74900 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLY A 252 REMARK 465 SER A 253 REMARK 465 ASN A 254 REMARK 465 THR A 255 REMARK 465 GLN A 256 REMARK 465 THR A 257 REMARK 465 VAL A 258 REMARK 465 LEU A 259 REMARK 465 PRO A 260 REMARK 465 PHE A 261 REMARK 465 THR A 262 REMARK 465 GLY A 263 REMARK 465 LEU A 264 REMARK 465 ASN A 265 REMARK 465 THR A 266 REMARK 465 PRO A 267 REMARK 465 ASN A 268 REMARK 465 GLY A 269 REMARK 465 VAL A 270 REMARK 465 ALA A 271 REMARK 465 VAL A 272 REMARK 465 ASP A 273 REMARK 465 SER A 274 REMARK 465 ALA A 275 REMARK 465 GLY A 276 REMARK 465 THR A 277 REMARK 465 VAL A 278 REMARK 465 TYR A 279 REMARK 465 VAL A 280 REMARK 465 THR A 281 REMARK 465 ASP A 282 REMARK 465 HIS A 283 REMARK 465 GLY A 284 REMARK 465 ASN A 285 REMARK 465 ASN A 286 REMARK 465 ARG A 287 REMARK 465 VAL A 288 REMARK 465 VAL A 289 REMARK 465 LYS A 290 REMARK 465 LEU A 291 REMARK 465 ALA A 292 REMARK 465 ALA A 293 REMARK 465 GLY A 294 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 48.74 -79.91 REMARK 500 THR A 56 79.07 73.68 REMARK 500 PRO A 92 49.51 -77.54 REMARK 500 THR A 98 85.43 68.45 REMARK 500 ASN A 100 -88.90 -120.56 REMARK 500 PRO A 134 44.37 -81.20 REMARK 500 ASN A 226 -66.58 -133.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WW7 RELATED DB: PDB REMARK 900 RELATED ID: 3WW8 RELATED DB: PDB REMARK 900 RELATED ID: 3WW9 RELATED DB: PDB REMARK 900 RELATED ID: 3WWB RELATED DB: PDB REMARK 900 RELATED ID: 3WWF RELATED DB: PDB DBREF 3WWA A -3 294 PDB 3WWA 3WWA -3 294 SEQRES 1 A 298 GLY SER HIS MET SER ASN THR GLN THR VAL LEU PRO PHE SEQRES 2 A 298 THR GLY LEU ASN THR PRO ASN GLY VAL ALA VAL ASP SER SEQRES 3 A 298 ALA GLY THR VAL TYR VAL THR ASP HIS GLY ASN ASN ARG SEQRES 4 A 298 VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR VAL SEQRES 5 A 298 LEU PRO PHE THR GLY LEU ASN THR PRO ASN GLY VAL ALA SEQRES 6 A 298 VAL ASP SER ALA GLY THR VAL TYR VAL THR ASP HIS GLY SEQRES 7 A 298 ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR SEQRES 8 A 298 GLN THR VAL LEU PRO PHE THR GLY LEU ASN THR PRO ASN SEQRES 9 A 298 GLY VAL ALA VAL ASP SER ALA GLY THR VAL TYR VAL THR SEQRES 10 A 298 ASP HIS GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SEQRES 11 A 298 SER ASN THR GLN THR VAL LEU PRO PHE THR GLY LEU ASN SEQRES 12 A 298 THR PRO ASN GLY VAL ALA VAL ASP SER ALA GLY THR VAL SEQRES 13 A 298 TYR VAL THR ASP HIS GLY ASN ASN ARG VAL VAL LYS LEU SEQRES 14 A 298 ALA ALA GLY SER ASN THR GLN THR VAL LEU PRO PHE THR SEQRES 15 A 298 GLY LEU ASN THR PRO ASN GLY VAL ALA VAL ASP SER ALA SEQRES 16 A 298 GLY THR VAL TYR VAL THR ASP HIS GLY ASN ASN ARG VAL SEQRES 17 A 298 VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR VAL LEU SEQRES 18 A 298 PRO PHE THR GLY LEU ASN THR PRO ASN GLY VAL ALA VAL SEQRES 19 A 298 ASP SER ALA GLY THR VAL TYR VAL THR ASP HIS GLY ASN SEQRES 20 A 298 ASN ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN SEQRES 21 A 298 THR VAL LEU PRO PHE THR GLY LEU ASN THR PRO ASN GLY SEQRES 22 A 298 VAL ALA VAL ASP SER ALA GLY THR VAL TYR VAL THR ASP SEQRES 23 A 298 HIS GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY HET IPA A 301 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 IPA C3 H8 O FORMUL 3 HOH *93(H2 O) HELIX 1 1 HIS A 31 ASN A 34 5 4 HELIX 2 2 GLY A 116 ASN A 118 5 3 HELIX 3 3 GLY A 158 ASN A 160 5 3 HELIX 4 4 GLY A 200 ASN A 202 5 3 HELIX 5 5 HIS A 241 ASN A 244 5 4 SHEET 1 A 4 THR A 5 VAL A 6 0 SHEET 2 A 4 ARG A 245 LEU A 249 -1 O LYS A 248 N THR A 5 SHEET 3 A 4 VAL A 236 ASP A 240 -1 N VAL A 238 O VAL A 247 SHEET 4 A 4 VAL A 228 VAL A 230 -1 N ALA A 229 O TYR A 237 SHEET 1 B 4 ALA A 19 VAL A 20 0 SHEET 2 B 4 VAL A 26 ASP A 30 -1 O TYR A 27 N ALA A 19 SHEET 3 B 4 ARG A 35 LEU A 39 -1 O VAL A 37 N VAL A 28 SHEET 4 B 4 THR A 47 VAL A 48 -1 O THR A 47 N LYS A 38 SHEET 1 C 4 PRO A 57 VAL A 62 0 SHEET 2 C 4 VAL A 68 ASP A 72 -1 O TYR A 69 N ALA A 61 SHEET 3 C 4 ARG A 77 LEU A 81 -1 O ARG A 77 N ASP A 72 SHEET 4 C 4 THR A 89 VAL A 90 -1 O THR A 89 N LYS A 80 SHEET 1 D 4 PRO A 99 VAL A 104 0 SHEET 2 D 4 VAL A 110 ASP A 114 -1 O TYR A 111 N ALA A 103 SHEET 3 D 4 ARG A 119 LEU A 123 -1 O ARG A 119 N ASP A 114 SHEET 4 D 4 THR A 131 VAL A 132 -1 O THR A 131 N LYS A 122 SHEET 1 E 4 PRO A 141 VAL A 146 0 SHEET 2 E 4 VAL A 152 ASP A 156 -1 O TYR A 153 N ALA A 145 SHEET 3 E 4 ARG A 161 LEU A 165 -1 O VAL A 163 N VAL A 154 SHEET 4 E 4 GLN A 172 VAL A 174 -1 O THR A 173 N LYS A 164 SHEET 1 F 4 PRO A 183 VAL A 188 0 SHEET 2 F 4 VAL A 194 ASP A 198 -1 O TYR A 195 N ALA A 187 SHEET 3 F 4 ARG A 203 LEU A 207 -1 O VAL A 205 N VAL A 196 SHEET 4 F 4 GLN A 214 VAL A 216 -1 O THR A 215 N LYS A 206 SITE 1 AC1 5 GLY A 11 ASN A 33 GLY A 95 LEU A 96 SITE 2 AC1 5 ASN A 117 CRYST1 40.056 69.498 92.301 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 0.024965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010834 0.00000