HEADER DE NOVO PROTEIN 26-NOV-19 6TJG TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED CAKE8 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAKE8; 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 BETA-PROPELLER, COMPUTATIONALLY DESIGNED, SYMMETRICAL, REPEAT KEYWDS 2 PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.LAIER,B.MYLEMANS,H.NOGUCHI,A.R.D.VOET REVDAT 3 01-MAY-24 6TJG 1 REMARK REVDAT 2 27-JAN-21 6TJG 1 JRNL REVDAT 1 06-MAY-20 6TJG 0 JRNL AUTH B.MYLEMANS,I.LAIER,K.KAMATA,S.AKASHI,H.NOGUCHI,J.R.H.TAME, JRNL AUTH 2 A.R.D.VOET JRNL TITL STRUCTURAL PLASTICITY OF A DESIGNER PROTEIN SHEDS LIGHT ON JRNL TITL 2 BETA-PROPELLER PROTEIN EVOLUTION. JRNL REF FEBS J. V. 288 530 2021 JRNL REFN ISSN 1742-464X JRNL PMID 32343866 JRNL DOI 10.1111/FEBS.15347 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 29276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.560 REMARK 3 FREE R VALUE TEST SET COUNT : 1627 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 35.4800 - 4.1200 1.00 2363 148 0.1378 0.1720 REMARK 3 2 4.1200 - 3.2700 0.99 2331 131 0.1422 0.1841 REMARK 3 3 3.2700 - 2.8600 0.99 2232 186 0.1838 0.2394 REMARK 3 4 2.8600 - 2.6000 1.00 2329 140 0.2065 0.2620 REMARK 3 5 2.6000 - 2.4100 1.00 2293 145 0.1950 0.2291 REMARK 3 6 2.4100 - 2.2700 1.00 2288 132 0.1976 0.2605 REMARK 3 7 2.2700 - 2.1500 0.99 2320 105 0.2001 0.2699 REMARK 3 8 2.1500 - 2.0600 1.00 2333 114 0.2082 0.2556 REMARK 3 9 2.0600 - 1.9800 1.00 2298 143 0.2246 0.3205 REMARK 3 10 1.9800 - 1.9100 0.99 2260 127 0.2179 0.2936 REMARK 3 11 1.9100 - 1.8500 0.99 2319 147 0.2373 0.3005 REMARK 3 12 1.8500 - 1.8000 0.99 2283 109 0.2447 0.3004 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) : 0.183 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.96 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 : 0.013 2525 REMARK 3 ANGLE : 1.235 3434 REMARK 3 CHIRALITY : 0.078 357 REMARK 3 PLANARITY : 0.008 450 REMARK 3 DIHEDRAL : 21.302 897 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 6TJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292104999. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-18 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 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 : 29356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 48.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.35600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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: COMPUTATIONALLY DESIGNED MODEL CAKE8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.18M MAGNESIUM ACETATE, 0.09M SODIUM, REMARK 280 CACODYLATE PH 6.5, 27% MPD, 15% GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K 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 32.94850 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: 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 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 N ASP A 1 OXT PRO A 320 1.66 REMARK 500 N ASP A 1 C PRO A 320 2.11 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 A 723 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A 724 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 725 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 726 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 727 DISTANCE = 6.73 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 403 DBREF 6TJG A -3 320 PDB 6TJG 6TJG -3 320 SEQRES 1 A 324 GLY SER HIS MET ASP GLY THR GLU LYS TRP ARG PHE LYS SEQRES 2 A 324 THR GLY LYS ALA ILE GLU ALA SER PRO VAL ILE GLY GLU SEQRES 3 A 324 ASP GLY THR ILE TYR VAL GLY SER ASN ASP GLY HIS LEU SEQRES 4 A 324 TYR ALA ILE ASN PRO ASP GLY THR GLU LYS TRP ARG PHE SEQRES 5 A 324 LYS THR GLY LYS ALA ILE GLU ALA SER PRO VAL ILE GLY SEQRES 6 A 324 GLU ASP GLY THR ILE TYR VAL GLY SER ASN ASP GLY HIS SEQRES 7 A 324 LEU TYR ALA ILE ASN PRO ASP GLY THR GLU LYS TRP ARG SEQRES 8 A 324 PHE LYS THR GLY LYS ALA ILE GLU ALA SER PRO VAL ILE SEQRES 9 A 324 GLY GLU ASP GLY THR ILE TYR VAL GLY SER ASN ASP GLY SEQRES 10 A 324 HIS LEU TYR ALA ILE ASN PRO ASP GLY THR GLU LYS TRP SEQRES 11 A 324 ARG PHE LYS THR GLY LYS ALA ILE GLU ALA SER PRO VAL SEQRES 12 A 324 ILE GLY GLU ASP GLY THR ILE TYR VAL GLY SER ASN ASP SEQRES 13 A 324 GLY HIS LEU TYR ALA ILE ASN PRO ASP GLY THR GLU LYS SEQRES 14 A 324 TRP ARG PHE LYS THR GLY LYS ALA ILE GLU ALA SER PRO SEQRES 15 A 324 VAL ILE GLY GLU ASP GLY THR ILE TYR VAL GLY SER ASN SEQRES 16 A 324 ASP GLY HIS LEU TYR ALA ILE ASN PRO ASP GLY THR GLU SEQRES 17 A 324 LYS TRP ARG PHE LYS THR GLY LYS ALA ILE GLU ALA SER SEQRES 18 A 324 PRO VAL ILE GLY GLU ASP GLY THR ILE TYR VAL GLY SER SEQRES 19 A 324 ASN ASP GLY HIS LEU TYR ALA ILE ASN PRO ASP GLY THR SEQRES 20 A 324 GLU LYS TRP ARG PHE LYS THR GLY LYS ALA ILE GLU ALA SEQRES 21 A 324 SER PRO VAL ILE GLY GLU ASP GLY THR ILE TYR VAL GLY SEQRES 22 A 324 SER ASN ASP GLY HIS LEU TYR ALA ILE ASN PRO ASP GLY SEQRES 23 A 324 THR GLU LYS TRP ARG PHE LYS THR GLY LYS ALA ILE GLU SEQRES 24 A 324 ALA SER PRO VAL ILE GLY GLU ASP GLY THR ILE TYR VAL SEQRES 25 A 324 GLY SER ASN ASP GLY HIS LEU TYR ALA ILE ASN PRO HET MPD A 401 8 HET MPD A 402 8 HET MPD A 403 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD 3(C6 H14 O2) FORMUL 5 HOH *227(H2 O) SHEET 1 AA1 4 GLU A 4 LYS A 9 0 SHEET 2 AA1 4 HIS A 314 ILE A 318 -1 O ALA A 317 N LYS A 5 SHEET 3 AA1 4 ILE A 306 GLY A 309 -1 N ILE A 306 O ILE A 318 SHEET 4 AA1 4 VAL A 299 ILE A 300 -1 N VAL A 299 O TYR A 307 SHEET 1 AA2 4 VAL A 19 ILE A 20 0 SHEET 2 AA2 4 ILE A 26 GLY A 29 -1 O TYR A 27 N VAL A 19 SHEET 3 AA2 4 HIS A 34 ILE A 38 -1 O ILE A 38 N ILE A 26 SHEET 4 AA2 4 GLU A 44 LYS A 49 -1 O LYS A 45 N ALA A 37 SHEET 1 AA3 4 VAL A 59 ILE A 60 0 SHEET 2 AA3 4 ILE A 66 GLY A 69 -1 O TYR A 67 N VAL A 59 SHEET 3 AA3 4 HIS A 74 ILE A 78 -1 O ILE A 78 N ILE A 66 SHEET 4 AA3 4 GLU A 84 LYS A 89 -1 O LYS A 85 N ALA A 77 SHEET 1 AA4 4 VAL A 99 ILE A 100 0 SHEET 2 AA4 4 ILE A 106 GLY A 109 -1 O TYR A 107 N VAL A 99 SHEET 3 AA4 4 HIS A 114 ILE A 118 -1 O TYR A 116 N VAL A 108 SHEET 4 AA4 4 GLU A 124 LYS A 129 -1 O LYS A 125 N ALA A 117 SHEET 1 AA5 4 VAL A 139 ILE A 140 0 SHEET 2 AA5 4 ILE A 146 GLY A 149 -1 O TYR A 147 N VAL A 139 SHEET 3 AA5 4 HIS A 154 ILE A 158 -1 O TYR A 156 N VAL A 148 SHEET 4 AA5 4 GLU A 164 LYS A 169 -1 O LYS A 165 N ALA A 157 SHEET 1 AA6 4 VAL A 179 ILE A 180 0 SHEET 2 AA6 4 ILE A 186 GLY A 189 -1 O TYR A 187 N VAL A 179 SHEET 3 AA6 4 HIS A 194 ILE A 198 -1 O ILE A 198 N ILE A 186 SHEET 4 AA6 4 GLU A 204 LYS A 209 -1 O LYS A 205 N ALA A 197 SHEET 1 AA7 4 VAL A 219 ILE A 220 0 SHEET 2 AA7 4 ILE A 226 GLY A 229 -1 O TYR A 227 N VAL A 219 SHEET 3 AA7 4 HIS A 234 ILE A 238 -1 O TYR A 236 N VAL A 228 SHEET 4 AA7 4 GLU A 244 LYS A 249 -1 O LYS A 245 N ALA A 237 SHEET 1 AA8 4 VAL A 259 ILE A 260 0 SHEET 2 AA8 4 ILE A 266 GLY A 269 -1 O TYR A 267 N VAL A 259 SHEET 3 AA8 4 HIS A 274 ILE A 278 -1 O TYR A 276 N VAL A 268 SHEET 4 AA8 4 GLU A 284 LYS A 289 -1 O LYS A 285 N ALA A 277 SITE 1 AC1 5 LYS A 49 ASP A 72 TYR A 76 ARG A 87 SITE 2 AC1 5 HOH A 588 SITE 1 AC2 4 GLU A 4 TRP A 6 ARG A 7 HOH A 662 SITE 1 AC3 3 ASN A 199 PRO A 200 ASP A 201 CRYST1 34.368 65.897 71.027 90.00 92.64 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 0.029097 0.000000 0.001342 0.00000 SCALE2 0.000000 0.015175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014094 0.00000