HEADER UNKNOWN FUNCTION 23-JUN-23 8PJS TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED SAKE6CEREF PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAKECEREF; 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 COMPUTATIONAL, DESIGN, SCAFFOLD, PROPELLER, KELCH, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.M.L.WOUTERS REVDAT 1 10-JUL-24 8PJS 0 JRNL AUTH S.M.L.WOUTERS,H.NOGUCHI,A.R.D.VOET JRNL TITL COMPUTATIONAL DESIGN OF THE SAKE SCAFFOLD PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 30454 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1555 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 48.3800 - 3.7800 1.00 2829 125 0.1333 0.1210 REMARK 3 2 3.7800 - 3.0000 1.00 2652 168 0.1549 0.1704 REMARK 3 3 3.0000 - 2.6200 1.00 2643 131 0.1681 0.2045 REMARK 3 4 2.6200 - 2.3800 1.00 2625 149 0.1672 0.1880 REMARK 3 5 2.3800 - 2.2100 1.00 2609 146 0.1579 0.1892 REMARK 3 6 2.2100 - 2.0800 1.00 2571 169 0.1594 0.2083 REMARK 3 7 2.0800 - 1.9800 1.00 2604 138 0.1550 0.1684 REMARK 3 8 1.9800 - 1.8900 1.00 2573 146 0.1591 0.2164 REMARK 3 9 1.8900 - 1.8200 1.00 2611 123 0.1838 0.1976 REMARK 3 10 1.8200 - 1.7600 1.00 2574 157 0.1975 0.2346 REMARK 3 11 1.7500 - 1.7000 1.00 2608 103 0.2372 0.2817 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) : 0.187 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.33 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 : 0.006 2108 REMARK 3 ANGLE : 0.930 2927 REMARK 3 CHIRALITY : 0.074 329 REMARK 3 PLANARITY : 0.006 393 REMARK 3 DIHEDRAL : 17.259 722 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 8PJS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-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 : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979510 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 1.10400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09 M HEPES SODIUM SALT PH 7.5, 1.26 REMARK 280 M TRI-SODIUM CITRATE, 10% (V/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 42.63367 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 85.26733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.26733 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 42.63367 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 525 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 GLY A 5 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 108 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 120 CG CD OE1 OE2 REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 GLU A 258 CG CD OE1 OE2 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 VAL A 127 -168.31 -125.39 REMARK 500 REMARK 500 REMARK: NULL DBREF 8PJS A 1 280 PDB 8PJS 8PJS 1 280 SEQRES 1 A 280 GLY SER HIS MET GLY GLY LEU ILE TYR ALA VAL GLY GLY SEQRES 2 A 280 ASP GLY HIS THR HIS LEU SER SER VAL GLU ALA TYR ASN SEQRES 3 A 280 PRO GLU THR ASN GLU TRP SER PRO VAL ALA PRO MET SER SEQRES 4 A 280 VAL PRO ARG SER GLY VAL GLY VAL ALA VAL ILE GLY GLY SEQRES 5 A 280 LEU ILE TYR ALA VAL GLY GLY ASP GLY HIS THR HIS LEU SEQRES 6 A 280 SER SER VAL GLU ALA TYR ASN PRO GLU THR ASN GLU TRP SEQRES 7 A 280 SER PRO VAL ALA PRO MET SER VAL PRO ARG SER GLY VAL SEQRES 8 A 280 GLY VAL ALA VAL ILE GLY GLY LEU ILE TYR ALA VAL GLY SEQRES 9 A 280 GLY ASP GLY HIS THR HIS LEU SER SER VAL GLU ALA TYR SEQRES 10 A 280 ASN PRO GLU THR ASN GLU TRP SER PRO VAL ALA PRO MET SEQRES 11 A 280 SER VAL PRO ARG SER GLY VAL GLY VAL ALA VAL ILE GLY SEQRES 12 A 280 GLY LEU ILE TYR ALA VAL GLY GLY ASP GLY HIS THR HIS SEQRES 13 A 280 LEU SER SER VAL GLU ALA TYR ASN PRO GLU THR ASN GLU SEQRES 14 A 280 TRP SER PRO VAL ALA PRO MET SER VAL PRO ARG SER GLY SEQRES 15 A 280 VAL GLY VAL ALA VAL ILE GLY GLY LEU ILE TYR ALA VAL SEQRES 16 A 280 GLY GLY ASP GLY HIS THR HIS LEU SER SER VAL GLU ALA SEQRES 17 A 280 TYR ASN PRO GLU THR ASN GLU TRP SER PRO VAL ALA PRO SEQRES 18 A 280 MET SER VAL PRO ARG SER GLY VAL GLY VAL ALA VAL ILE SEQRES 19 A 280 GLY GLY LEU ILE TYR ALA VAL GLY GLY ASP GLY HIS THR SEQRES 20 A 280 HIS LEU SER SER VAL GLU ALA TYR ASN PRO GLU THR ASN SEQRES 21 A 280 GLU TRP SER PRO VAL ALA PRO MET SER VAL PRO ARG SER SEQRES 22 A 280 GLY VAL GLY VAL ALA VAL ILE FORMUL 2 HOH *257(H2 O) SHEET 1 AA1 4 GLU A 31 VAL A 35 0 SHEET 2 AA1 4 VAL A 22 ASN A 26 -1 N ALA A 24 O SER A 33 SHEET 3 AA1 4 LEU A 7 VAL A 11 -1 N ILE A 8 O TYR A 25 SHEET 4 AA1 4 GLY A 276 ILE A 280 -1 O GLY A 276 N VAL A 11 SHEET 1 AA2 4 GLY A 46 ILE A 50 0 SHEET 2 AA2 4 LEU A 53 VAL A 57 -1 O TYR A 55 N ALA A 48 SHEET 3 AA2 4 VAL A 68 ASN A 72 -1 O GLU A 69 N ALA A 56 SHEET 4 AA2 4 GLU A 77 VAL A 81 -1 O SER A 79 N ALA A 70 SHEET 1 AA3 4 GLY A 92 ILE A 96 0 SHEET 2 AA3 4 LEU A 99 VAL A 103 -1 O VAL A 103 N GLY A 92 SHEET 3 AA3 4 VAL A 114 ASN A 118 -1 O GLU A 115 N ALA A 102 SHEET 4 AA3 4 GLU A 123 VAL A 127 -1 O SER A 125 N ALA A 116 SHEET 1 AA4 4 GLY A 138 ILE A 142 0 SHEET 2 AA4 4 LEU A 145 VAL A 149 -1 O VAL A 149 N GLY A 138 SHEET 3 AA4 4 VAL A 160 ASN A 164 -1 O GLU A 161 N ALA A 148 SHEET 4 AA4 4 GLU A 169 VAL A 173 -1 O SER A 171 N ALA A 162 SHEET 1 AA5 4 GLY A 184 ILE A 188 0 SHEET 2 AA5 4 LEU A 191 VAL A 195 -1 O TYR A 193 N ALA A 186 SHEET 3 AA5 4 VAL A 206 TYR A 209 -1 O TYR A 209 N ILE A 192 SHEET 4 AA5 4 TRP A 216 VAL A 219 -1 O SER A 217 N ALA A 208 SHEET 1 AA6 4 GLY A 230 ILE A 234 0 SHEET 2 AA6 4 LEU A 237 VAL A 241 -1 O VAL A 241 N GLY A 230 SHEET 3 AA6 4 VAL A 252 ASN A 256 -1 O GLU A 253 N ALA A 240 SHEET 4 AA6 4 GLU A 261 VAL A 265 -1 O SER A 263 N ALA A 254 CRYST1 60.346 60.346 127.901 90.00 90.00 120.00 P 31 2 1 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 0.016571 0.009567 0.000000 0.00000 SCALE2 0.000000 0.019135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007819 0.00000