HEADER UNKNOWN FUNCTION 23-JUN-23 8PJY TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED SAKE6EEREF PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAKE6EEREF; 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 8PJY 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 64763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 3265 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 42.7600 - 3.7000 1.00 2718 164 0.1480 0.1572 REMARK 3 2 3.7000 - 2.9300 1.00 2705 127 0.1394 0.1537 REMARK 3 3 2.9300 - 2.5600 1.00 2674 163 0.1320 0.1411 REMARK 3 4 2.5600 - 2.3300 1.00 2683 146 0.1380 0.1534 REMARK 3 5 2.3300 - 2.1600 1.00 2673 151 0.1219 0.1497 REMARK 3 6 2.1600 - 2.0300 1.00 2679 141 0.1231 0.1536 REMARK 3 7 2.0300 - 1.9300 1.00 2696 129 0.1155 0.1331 REMARK 3 8 1.9300 - 1.8500 1.00 2663 160 0.1220 0.1421 REMARK 3 9 1.8500 - 1.7800 1.00 2648 142 0.1270 0.1385 REMARK 3 10 1.7800 - 1.7200 1.00 2676 151 0.1263 0.1541 REMARK 3 11 1.7200 - 1.6600 1.00 2643 169 0.1244 0.1470 REMARK 3 12 1.6600 - 1.6100 1.00 2663 142 0.1216 0.1535 REMARK 3 13 1.6100 - 1.5700 1.00 2693 119 0.1221 0.1533 REMARK 3 14 1.5700 - 1.5300 1.00 2680 145 0.1199 0.1395 REMARK 3 15 1.5300 - 1.5000 1.00 2671 139 0.1284 0.1685 REMARK 3 16 1.5000 - 1.4700 1.00 2686 110 0.1407 0.1585 REMARK 3 17 1.4700 - 1.4400 1.00 2672 153 0.1577 0.2052 REMARK 3 18 1.4400 - 1.4100 1.00 2636 157 0.1603 0.1982 REMARK 3 19 1.4100 - 1.3900 1.00 2652 121 0.1623 0.1857 REMARK 3 20 1.3900 - 1.3600 1.00 2716 126 0.1725 0.2133 REMARK 3 21 1.3600 - 1.3400 1.00 2612 158 0.1772 0.2198 REMARK 3 22 1.3400 - 1.3200 1.00 2697 128 0.1809 0.1845 REMARK 3 23 1.3200 - 1.3000 1.00 2662 124 0.2028 0.2254 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) : 0.102 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.407 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.62 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 : 0.008 2223 REMARK 3 ANGLE : 1.127 3063 REMARK 3 CHIRALITY : 0.095 343 REMARK 3 PLANARITY : 0.009 404 REMARK 3 DIHEDRAL : 11.492 755 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 8PJY 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_1292131408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-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) : 0.978570 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 : 64797 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 42.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.64500 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 (%): 43.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, 25 % PEG 3350, VAPOR DIFFUSION, 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 33.33050 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 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 GLY A 5 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 HIS A 68 -39.22 -138.63 REMARK 500 HIS A 166 -32.59 -148.48 REMARK 500 VAL A 185 -168.85 -117.99 REMARK 500 HIS A 264 -31.17 -140.44 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 627 DISTANCE = 6.55 ANGSTROMS DBREF 8PJY A 1 298 PDB 8PJY 8PJY 1 298 SEQRES 1 A 298 GLY SER HIS MET GLY GLY LEU ILE TYR ALA VAL GLY GLY SEQRES 2 A 298 TYR ASN ASN SER PRO ASP GLY HIS THR HIS LEU SER SER SEQRES 3 A 298 LEU GLU ALA TYR ASN PRO SER THR ASP THR TRP SER PRO SEQRES 4 A 298 VAL ALA PRO MET SER VAL PRO ARG SER GLY VAL GLY VAL SEQRES 5 A 298 ALA VAL ILE ASP GLY LEU ILE TYR ALA VAL GLY GLY TYR SEQRES 6 A 298 ASP GLY HIS THR HIS LEU ASN SER VAL GLU ALA TYR ASP SEQRES 7 A 298 PRO GLU THR ASP GLU TRP SER LEU VAL ALA PRO MET THR SEQRES 8 A 298 THR ARG ARG SER GLY VAL GLY VAL ALA VAL LEU GLY GLY SEQRES 9 A 298 LEU ILE TYR ALA VAL GLY GLY TYR ASN ASN SER PRO ASP SEQRES 10 A 298 GLY HIS THR HIS LEU SER SER LEU GLU ALA TYR ASN PRO SEQRES 11 A 298 SER THR ASP THR TRP SER PRO VAL ALA PRO MET SER VAL SEQRES 12 A 298 PRO ARG SER GLY VAL GLY VAL ALA VAL ILE ASP GLY LEU SEQRES 13 A 298 ILE TYR ALA VAL GLY GLY TYR ASP GLY HIS THR HIS LEU SEQRES 14 A 298 ASN SER VAL GLU ALA TYR ASP PRO GLU THR ASP GLU TRP SEQRES 15 A 298 SER LEU VAL ALA PRO MET THR THR ARG ARG SER GLY VAL SEQRES 16 A 298 GLY VAL ALA VAL LEU GLY GLY LEU ILE TYR ALA VAL GLY SEQRES 17 A 298 GLY TYR ASN ASN SER PRO ASP GLY HIS THR HIS LEU SER SEQRES 18 A 298 SER LEU GLU ALA TYR ASN PRO SER THR ASP THR TRP SER SEQRES 19 A 298 PRO VAL ALA PRO MET SER VAL PRO ARG SER GLY VAL GLY SEQRES 20 A 298 VAL ALA VAL ILE ASP GLY LEU ILE TYR ALA VAL GLY GLY SEQRES 21 A 298 TYR ASP GLY HIS THR HIS LEU ASN SER VAL GLU ALA TYR SEQRES 22 A 298 ASP PRO GLU THR ASP GLU TRP SER LEU VAL ALA PRO MET SEQRES 23 A 298 THR THR ARG ARG SER GLY VAL GLY VAL ALA VAL LEU FORMUL 2 HOH *327(H2 O) SHEET 1 AA1 4 THR A 36 VAL A 40 0 SHEET 2 AA1 4 LEU A 27 ASN A 31 -1 N ALA A 29 O SER A 38 SHEET 3 AA1 4 LEU A 7 VAL A 11 -1 N ILE A 8 O TYR A 30 SHEET 4 AA1 4 GLY A 294 LEU A 298 -1 O ALA A 296 N TYR A 9 SHEET 1 AA2 2 TYR A 14 ASN A 15 0 SHEET 2 AA2 2 THR A 22 HIS A 23 -1 O THR A 22 N ASN A 15 SHEET 1 AA3 4 GLY A 51 ILE A 55 0 SHEET 2 AA3 4 LEU A 58 VAL A 62 -1 O TYR A 60 N ALA A 53 SHEET 3 AA3 4 VAL A 74 ASP A 78 -1 O GLU A 75 N ALA A 61 SHEET 4 AA3 4 GLU A 83 LEU A 86 -1 O SER A 85 N ALA A 76 SHEET 1 AA4 4 GLY A 98 LEU A 102 0 SHEET 2 AA4 4 LEU A 105 VAL A 109 -1 O TYR A 107 N ALA A 100 SHEET 3 AA4 4 LEU A 125 TYR A 128 -1 O TYR A 128 N ILE A 106 SHEET 4 AA4 4 TRP A 135 VAL A 138 -1 O SER A 136 N ALA A 127 SHEET 1 AA5 2 TYR A 112 ASN A 113 0 SHEET 2 AA5 2 THR A 120 HIS A 121 -1 O THR A 120 N ASN A 113 SHEET 1 AA6 4 GLY A 149 ILE A 153 0 SHEET 2 AA6 4 LEU A 156 VAL A 160 -1 O TYR A 158 N ALA A 151 SHEET 3 AA6 4 VAL A 172 ASP A 176 -1 O GLU A 173 N ALA A 159 SHEET 4 AA6 4 GLU A 181 LEU A 184 -1 O SER A 183 N ALA A 174 SHEET 1 AA7 4 GLY A 196 LEU A 200 0 SHEET 2 AA7 4 LEU A 203 VAL A 207 -1 O TYR A 205 N ALA A 198 SHEET 3 AA7 4 LEU A 223 ASN A 227 -1 O TYR A 226 N ILE A 204 SHEET 4 AA7 4 THR A 232 VAL A 236 -1 O SER A 234 N ALA A 225 SHEET 1 AA8 2 TYR A 210 SER A 213 0 SHEET 2 AA8 2 GLY A 216 HIS A 219 -1 O THR A 218 N ASN A 211 SHEET 1 AA9 4 GLY A 247 ILE A 251 0 SHEET 2 AA9 4 LEU A 254 VAL A 258 -1 O TYR A 256 N ALA A 249 SHEET 3 AA9 4 VAL A 270 ASP A 274 -1 O TYR A 273 N ILE A 255 SHEET 4 AA9 4 GLU A 279 VAL A 283 -1 O SER A 281 N ALA A 272 CISPEP 1 SER A 17 PRO A 18 0 4.94 CRYST1 47.048 66.661 48.243 90.00 117.59 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 0.021255 0.000000 0.011107 0.00000 SCALE2 0.000000 0.015001 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023388 0.00000