HEADER DE NOVO PROTEIN 05-NOV-18 6I38 TITLE CRYSTAL STRUCTURE OF NV2PIZZA6-AYW, A CIRCULARLY PERMUTED DESIGNER TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NV2PIZZA6-AYW; 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 BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS CIRCULARLY PERMUTED DESIGNER PROTEIN, ARTIFICIAL PROTEIN, BETA- KEYWDS 2 PROPELLER, PIZZA, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.MYLEMANS,H.NOGUCHI,E.DERIDDER,A.R.D.VOET REVDAT 3 24-JAN-24 6I38 1 REMARK REVDAT 2 21-OCT-20 6I38 1 JRNL REVDAT 1 20-NOV-19 6I38 0 JRNL AUTH B.MYLEMANS,H.NOGUCHI,E.DERIDDER,E.LESCRINIER,J.R.H.TAME, JRNL AUTH 2 A.R.D.VOET JRNL TITL INFLUENCE OF CIRCULAR PERMUTATIONS ON THE STRUCTURE AND JRNL TITL 2 STABILITY OF A SIX-FOLD CIRCULAR SYMMETRIC DESIGNER PROTEIN. JRNL REF PROTEIN SCI. 2020 JRNL REFN ESSN 1469-896X JRNL PMID 33006397 JRNL DOI 10.1002/PRO.3961 REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 27584 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1387 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 44.3574 - 3.4036 1.00 2811 144 0.1446 0.1549 REMARK 3 2 3.4036 - 2.7016 1.00 2695 123 0.1599 0.1932 REMARK 3 3 2.7016 - 2.3602 1.00 2654 136 0.1752 0.2022 REMARK 3 4 2.3602 - 2.1444 1.00 2612 138 0.1757 0.2276 REMARK 3 5 2.1444 - 1.9907 0.99 2602 142 0.1780 0.2295 REMARK 3 6 1.9907 - 1.8733 0.99 2621 127 0.1876 0.2188 REMARK 3 7 1.8733 - 1.7795 0.99 2546 169 0.1906 0.2548 REMARK 3 8 1.7795 - 1.7020 0.99 2557 135 0.2076 0.2679 REMARK 3 9 1.7020 - 1.6365 0.98 2569 136 0.2187 0.2699 REMARK 3 10 1.6365 - 1.5800 0.97 2530 137 0.2228 0.2582 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.370 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 : 0.004 2045 REMARK 3 ANGLE : 0.766 2864 REMARK 3 CHIRALITY : 0.056 365 REMARK 3 PLANARITY : 0.006 384 REMARK 3 DIHEDRAL : 2.759 1490 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 6I38 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200012564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-17 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27640 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 44.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 6F0Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% (W/V) PEG3350 0.1M BIS-TRIS PH5.5 REMARK 280 +20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292.15K 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 24.64750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.91350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.69850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.91350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.64750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.69850 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10200 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 8 REMARK 465 SER A 9 REMARK 465 HIS A 10 REMARK 465 MET A 11 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 THR A 14 65.06 39.96 REMARK 500 SER A 16 -66.90 -107.25 REMARK 500 PRO A 50 44.03 -81.71 REMARK 500 SER A 58 -78.29 -109.32 REMARK 500 SER A 58 -86.91 -109.92 REMARK 500 PRO A 92 42.83 -84.43 REMARK 500 PRO A 134 40.52 -81.48 REMARK 500 THR A 140 59.65 39.19 REMARK 500 SER A 142 -64.11 -108.85 REMARK 500 PRO A 176 47.03 -79.74 REMARK 500 SER A 184 -84.01 -116.33 REMARK 500 PRO A 218 45.81 -79.26 REMARK 500 PRO A 218 45.81 -79.90 REMARK 500 THR A 224 56.60 37.70 REMARK 500 PRO A 260 45.34 -81.72 REMARK 500 REMARK 500 REMARK: NULL DBREF 6I38 A 8 262 PDB 6I38 6I38 8 262 SEQRES 1 A 255 GLY SER HIS MET LEU ASN THR PRO SER GLY VAL ALA VAL SEQRES 2 A 255 ASP SER ALA GLY THR VAL TRP VAL THR ASP HIS GLY ASN SEQRES 3 A 255 ASN ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN SEQRES 4 A 255 THR VAL LEU PRO PHE THR GLY LEU ASN THR PRO SER GLY SEQRES 5 A 255 VAL ALA VAL ASP SER ALA GLY THR VAL TRP VAL THR ASP SEQRES 6 A 255 HIS GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SER SEQRES 7 A 255 ASN THR GLN THR VAL LEU PRO PHE THR GLY LEU ASN THR SEQRES 8 A 255 PRO SER GLY VAL ALA VAL ASP SER ALA GLY THR VAL TRP SEQRES 9 A 255 VAL THR ASP HIS GLY ASN ASN ARG VAL VAL LYS LEU ALA SEQRES 10 A 255 ALA GLY SER ASN THR GLN THR VAL LEU PRO PHE THR GLY SEQRES 11 A 255 LEU ASN THR PRO SER GLY VAL ALA VAL ASP SER ALA GLY SEQRES 12 A 255 THR VAL TRP VAL THR ASP HIS GLY ASN ASN ARG VAL VAL SEQRES 13 A 255 LYS LEU ALA ALA GLY SER ASN THR GLN THR VAL LEU PRO SEQRES 14 A 255 PHE THR GLY LEU ASN THR PRO SER GLY VAL ALA VAL ASP SEQRES 15 A 255 SER ALA GLY THR VAL TRP VAL THR ASP HIS GLY ASN ASN SEQRES 16 A 255 ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR SEQRES 17 A 255 VAL LEU PRO PHE THR GLY LEU ASN THR PRO SER GLY VAL SEQRES 18 A 255 ALA VAL ASP SER ALA GLY THR VAL TRP VAL THR ASP HIS SEQRES 19 A 255 GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SER ASN SEQRES 20 A 255 THR GLN THR VAL LEU PRO PHE THR FORMUL 2 HOH *296(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 VAL A 18 VAL A 20 0 SHEET 2 AA1 4 VAL A 26 ASP A 30 -1 O TRP A 27 N ALA A 19 SHEET 3 AA1 4 ARG A 35 LEU A 39 -1 O VAL A 37 N VAL A 28 SHEET 4 AA1 4 THR A 47 VAL A 48 -1 O THR A 47 N LYS A 38 SHEET 1 AA2 4 VAL A 60 VAL A 62 0 SHEET 2 AA2 4 VAL A 68 ASP A 72 -1 O TRP A 69 N ALA A 61 SHEET 3 AA2 4 ARG A 77 LEU A 81 -1 O VAL A 79 N VAL A 70 SHEET 4 AA2 4 THR A 89 VAL A 90 -1 O THR A 89 N LYS A 80 SHEET 1 AA3 4 ALA A 103 VAL A 104 0 SHEET 2 AA3 4 VAL A 110 ASP A 114 -1 O TRP A 111 N ALA A 103 SHEET 3 AA3 4 ARG A 119 LEU A 123 -1 O LEU A 123 N VAL A 110 SHEET 4 AA3 4 GLN A 130 VAL A 132 -1 O THR A 131 N LYS A 122 SHEET 1 AA4 4 VAL A 144 VAL A 146 0 SHEET 2 AA4 4 VAL A 152 ASP A 156 -1 O TRP A 153 N ALA A 145 SHEET 3 AA4 4 ARG A 161 LEU A 165 -1 O VAL A 163 N VAL A 154 SHEET 4 AA4 4 GLN A 172 VAL A 174 -1 O THR A 173 N LYS A 164 SHEET 1 AA5 4 VAL A 186 VAL A 188 0 SHEET 2 AA5 4 VAL A 194 ASP A 198 -1 O TRP A 195 N ALA A 187 SHEET 3 AA5 4 ARG A 203 LEU A 207 -1 O VAL A 205 N VAL A 196 SHEET 4 AA5 4 THR A 215 VAL A 216 -1 O THR A 215 N LYS A 206 SHEET 1 AA6 4 ALA A 229 VAL A 230 0 SHEET 2 AA6 4 VAL A 236 ASP A 240 -1 O TRP A 237 N ALA A 229 SHEET 3 AA6 4 ARG A 245 LEU A 249 -1 O VAL A 247 N VAL A 238 SHEET 4 AA6 4 THR A 257 VAL A 258 -1 O THR A 257 N LYS A 248 CRYST1 49.295 57.397 69.827 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 0.020286 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014321 0.00000