HEADER DE NOVO PROTEIN 01-APR-18 6G6P TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED IKA8 PROTEIN: TITLE 2 CRYSTAL PACKING NO.2 IN P63 COMPND MOL_ID: 1; COMPND 2 MOLECULE: IKA8; 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, DE NOVO PROTEIN, WD40 PROTEINS EXPDTA X-RAY DIFFRACTION AUTHOR H.NOGUCHI,C.ADDY,D.SIMONCINI,L.VAN MEERVELT,T.SCHIEX,K.Y.J.ZHANG, AUTHOR 2 J.R.H.TAME,A.R.D.VOET REVDAT 3 08-MAY-24 6G6P 1 REMARK REVDAT 2 13-FEB-19 6G6P 1 JRNL REVDAT 1 28-NOV-18 6G6P 0 JRNL AUTH H.NOGUCHI,C.ADDY,D.SIMONCINI,S.WOUTERS,B.MYLEMANS, JRNL AUTH 2 L.VAN MEERVELT,T.SCHIEX,K.Y.J.ZHANG,J.R.H.TAME,A.R.D.VOET JRNL TITL COMPUTATIONAL DESIGN OF SYMMETRICAL EIGHT-BLADED JRNL TITL 2 BETA-PROPELLER PROTEINS. JRNL REF IUCRJ V. 6 46 2019 JRNL REFN ESSN 2052-2525 JRNL PMID 30713702 JRNL DOI 10.1107/S205225251801480X REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19742 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) : 0.212 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 919 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 48.4153 - 4.5901 1.00 2757 148 0.1860 0.2337 REMARK 3 2 4.5901 - 3.6437 1.00 2691 138 0.1797 0.2487 REMARK 3 3 3.6437 - 3.1832 1.00 2685 132 0.2234 0.2623 REMARK 3 4 3.1832 - 2.8922 1.00 2686 117 0.2612 0.3135 REMARK 3 5 2.8922 - 2.6849 1.00 2676 125 0.2925 0.3204 REMARK 3 6 2.6849 - 2.5266 1.00 2656 131 0.2961 0.3793 REMARK 3 7 2.5266 - 2.4001 1.00 2672 128 0.2920 0.3516 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.190 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 : 0.003 2445 REMARK 3 ANGLE : 0.599 3324 REMARK 3 CHIRALITY : 0.058 395 REMARK 3 PLANARITY : 0.002 420 REMARK 3 DIHEDRAL : 4.878 1909 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 6G6P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19765 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 20.40 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 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 (%): 66.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH6.0, 1.0M LICL, 20% (W/V) REMARK 280 PEG6000, VAPOR DIFFUSION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.93450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.93450 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 26.93450 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: 13630 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 319 REMARK 465 THR A 320 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 LYS A 21 -120.70 58.54 REMARK 500 LYS A 101 -117.60 52.23 REMARK 500 GLU A 213 79.14 57.30 REMARK 500 ASP A 221 -133.65 55.19 REMARK 500 LYS A 261 -120.52 51.12 REMARK 500 ASN A 302 17.58 59.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 6G6P A -3 320 PDB 6G6P 6G6P -3 320 SEQRES 1 A 324 GLY SER HIS MET GLY GLN GLU LEU VAL SER LEU GLU GLY SEQRES 2 A 324 HIS GLN SER ALA ILE THR ALA LEU ALA PHE SER LYS ASN SEQRES 3 A 324 ILE VAL VAL SER GLY ALA ALA ASP GLY THR ILE LYS VAL SEQRES 4 A 324 TRP ASP ILE LEU THR GLY GLN LEU LEU ARG ASP HIS ASP SEQRES 5 A 324 GLY HIS GLN SER GLU VAL THR ALA LEU GLN PHE LYS ASP SEQRES 6 A 324 ASN ILE VAL VAL SER GLY ALA LYS ASP GLY THR VAL LYS SEQRES 7 A 324 VAL TRP TYR ILE GLY THR GLY GLN GLU LEU VAL SER LEU SEQRES 8 A 324 GLU GLY HIS GLN SER ALA ILE THR ALA LEU ALA PHE SER SEQRES 9 A 324 LYS ASN ILE VAL VAL SER GLY ALA ALA ASP GLY THR ILE SEQRES 10 A 324 LYS VAL TRP ASP ILE LEU THR GLY GLN LEU LEU ARG ASP SEQRES 11 A 324 HIS ASP GLY HIS GLN SER GLU VAL THR ALA LEU GLN PHE SEQRES 12 A 324 LYS ASP ASN ILE VAL VAL SER GLY ALA LYS ASP GLY THR SEQRES 13 A 324 VAL LYS VAL TRP TYR ILE GLY THR GLY GLN GLU LEU VAL SEQRES 14 A 324 SER LEU GLU GLY HIS GLN SER ALA ILE THR ALA LEU ALA SEQRES 15 A 324 PHE SER LYS ASN ILE VAL VAL SER GLY ALA ALA ASP GLY SEQRES 16 A 324 THR ILE LYS VAL TRP ASP ILE LEU THR GLY GLN LEU LEU SEQRES 17 A 324 ARG ASP HIS ASP GLY HIS GLN SER GLU VAL THR ALA LEU SEQRES 18 A 324 GLN PHE LYS ASP ASN ILE VAL VAL SER GLY ALA LYS ASP SEQRES 19 A 324 GLY THR VAL LYS VAL TRP TYR ILE GLY THR GLY GLN GLU SEQRES 20 A 324 LEU VAL SER LEU GLU GLY HIS GLN SER ALA ILE THR ALA SEQRES 21 A 324 LEU ALA PHE SER LYS ASN ILE VAL VAL SER GLY ALA ALA SEQRES 22 A 324 ASP GLY THR ILE LYS VAL TRP ASP ILE LEU THR GLY GLN SEQRES 23 A 324 LEU LEU ARG ASP HIS ASP GLY HIS GLN SER GLU VAL THR SEQRES 24 A 324 ALA LEU GLN PHE LYS ASP ASN ILE VAL VAL SER GLY ALA SEQRES 25 A 324 LYS ASP GLY THR VAL LYS VAL TRP TYR ILE GLY THR FORMUL 2 HOH *36(H2 O) SHEET 1 AA1 4 GLU A 3 LEU A 7 0 SHEET 2 AA1 4 VAL A 313 TYR A 317 -1 O VAL A 315 N LEU A 4 SHEET 3 AA1 4 ILE A 303 ALA A 308 -1 N VAL A 304 O TRP A 316 SHEET 4 AA1 4 VAL A 294 LYS A 300 -1 N GLN A 298 O VAL A 305 SHEET 1 AA2 4 ILE A 14 SER A 20 0 SHEET 2 AA2 4 ILE A 23 ALA A 28 -1 O VAL A 25 N ALA A 18 SHEET 3 AA2 4 ILE A 33 ASP A 37 -1 O TRP A 36 N VAL A 24 SHEET 4 AA2 4 GLN A 42 ASP A 46 -1 O GLN A 42 N ASP A 37 SHEET 1 AA3 4 VAL A 54 LYS A 60 0 SHEET 2 AA3 4 ILE A 63 ALA A 68 -1 O VAL A 65 N GLN A 58 SHEET 3 AA3 4 VAL A 73 TYR A 77 -1 O TRP A 76 N VAL A 64 SHEET 4 AA3 4 GLU A 83 SER A 86 -1 O LEU A 84 N VAL A 75 SHEET 1 AA4 4 ILE A 94 SER A 100 0 SHEET 2 AA4 4 ILE A 103 ALA A 108 -1 O GLY A 107 N THR A 95 SHEET 3 AA4 4 THR A 112 ASP A 117 -1 O TRP A 116 N VAL A 104 SHEET 4 AA4 4 LEU A 123 ASP A 128 -1 O ARG A 125 N VAL A 115 SHEET 1 AA5 4 VAL A 134 LYS A 140 0 SHEET 2 AA5 4 ILE A 143 ALA A 148 -1 O VAL A 145 N GLN A 138 SHEET 3 AA5 4 VAL A 153 TYR A 157 -1 O LYS A 154 N SER A 146 SHEET 4 AA5 4 GLU A 163 SER A 166 -1 O LEU A 164 N VAL A 155 SHEET 1 AA6 4 ILE A 174 PHE A 179 0 SHEET 2 AA6 4 ILE A 183 ALA A 188 -1 O GLY A 187 N THR A 175 SHEET 3 AA6 4 ILE A 193 ASP A 197 -1 O TRP A 196 N VAL A 184 SHEET 4 AA6 4 LEU A 203 HIS A 207 -1 O HIS A 207 N ILE A 193 SHEET 1 AA7 4 VAL A 214 LYS A 220 0 SHEET 2 AA7 4 ILE A 223 ALA A 228 -1 O GLY A 227 N THR A 215 SHEET 3 AA7 4 VAL A 233 TYR A 237 -1 O TRP A 236 N VAL A 224 SHEET 4 AA7 4 GLU A 243 SER A 246 -1 O LEU A 244 N VAL A 235 SHEET 1 AA8 4 ILE A 254 SER A 260 0 SHEET 2 AA8 4 ILE A 263 ALA A 268 -1 O GLY A 267 N THR A 255 SHEET 3 AA8 4 ILE A 273 ASP A 277 -1 O TRP A 276 N VAL A 264 SHEET 4 AA8 4 LEU A 283 HIS A 287 -1 O LEU A 284 N VAL A 275 CRYST1 127.374 127.374 53.869 90.00 90.00 120.00 P 63 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 0.007851 0.004533 0.000000 0.00000 SCALE2 0.000000 0.009065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018564 0.00000