HEADER UNKNOWN FUNCTION 29-MAY-21 7OP4 TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED SAKE6BE-3HH PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAKE6BE-3HH; 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(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-28A(+) KEYWDS BETA PROPELLER, SYNTHETIC, DESIGNER, LAYER, SELF-ASSEMBLY, UNKNOWN KEYWDS 2 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.M.L.WOUTERS,H.NOGUCHI,D.E.CLARKE,A.R.D.VOET,S.DE FEYTER REVDAT 2 01-MAY-24 7OP4 1 REMARK REVDAT 1 14-DEC-22 7OP4 0 JRNL AUTH S.M.L.WOUTERS,D.E.CLARKE,H.NOGUCHI,G.VELPULA,A.R.D.VOET, JRNL AUTH 2 S.DE FEYTER JRNL TITL SAKE: COMPUTATIONALLY DESIGNED MODULAR PROTEIN BUILDING JRNL TITL 2 BLOCKS FOR MACROMOLECULAR ASSEMBLIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2-4158 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 33207 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1644 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 38.1500 - 3.4800 0.97 2685 169 0.1683 0.1794 REMARK 3 2 3.4800 - 2.7600 0.99 2649 187 0.1789 0.1829 REMARK 3 3 2.7600 - 2.4100 0.97 2769 87 0.1847 0.2686 REMARK 3 4 2.4100 - 2.1900 0.94 2517 139 0.1923 0.1883 REMARK 3 5 2.1900 - 2.0400 0.97 2706 123 0.1802 0.2574 REMARK 3 6 2.0400 - 1.9200 0.97 2642 129 0.1861 0.2435 REMARK 3 7 1.9200 - 1.8200 0.96 2601 159 0.2037 0.2107 REMARK 3 8 1.8200 - 1.7400 0.97 2668 130 0.2044 0.2114 REMARK 3 9 1.7400 - 1.6700 0.92 2569 107 0.2118 0.1916 REMARK 3 10 1.6700 - 1.6200 0.95 2577 120 0.2129 0.2110 REMARK 3 11 1.6200 - 1.5600 0.95 2593 165 0.1986 0.2587 REMARK 3 12 1.5600 - 1.5200 0.95 2587 129 0.2056 0.2137 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.63 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7OP4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292116164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 38.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.20600 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: MOLREP REMARK 200 STARTING MODEL: DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 0.9 M NA PHOSPHATE, 0.9 M K REMARK 280 PHOSPHATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.02450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.14500 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: 10290 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 ASN A 5 REMARK 465 GLY A 6 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 ASN A 17 CG OD1 ND2 REMARK 470 ASN A 21 CG REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 ARG A 30 NE CZ NH1 NH2 REMARK 470 ARG A 42 NE CZ NH1 NH2 REMARK 470 ASN A 64 CG OD1 ND2 REMARK 470 HIS A 76 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 ARG A 89 NE CZ NH1 NH2 REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 ARG A 124 CD NE CZ NH1 NH2 REMARK 470 GLU A 126 CD OE1 OE2 REMARK 470 ASN A 158 CG OD1 ND2 REMARK 470 HIS A 170 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 217 CG CD OE1 OE2 REMARK 470 ARG A 218 NE CZ NH1 NH2 REMARK 470 GLU A 220 CG CD OE1 OE2 REMARK 470 ARG A 230 NE CZ NH1 NH2 REMARK 470 HIS A 264 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 267 CD OE1 OE2 REMARK 470 ARG A 277 NE CZ NH1 NH2 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 36 -159.62 -120.12 REMARK 500 VAL A 83 -159.39 -118.92 REMARK 500 VAL A 130 -159.75 -120.06 REMARK 500 VAL A 177 -159.66 -119.39 REMARK 500 VAL A 224 -159.19 -118.44 REMARK 500 VAL A 271 -160.61 -120.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 7OP4 A 1 286 PDB 7OP4 7OP4 1 286 SEQRES 1 A 286 GLY SER HIS MET ASN GLY LEU ILE TYR ALA VAL GLY GLY SEQRES 2 A 286 TYR ASP GLY ASN THR HIS LEU ASN SER VAL GLU ALA TYR SEQRES 3 A 286 ASP PRO GLU ARG ASN GLU TRP SER LEU VAL ALA PRO LEU SEQRES 4 A 286 SER THR ARG ARG SER GLY VAL GLY VAL ALA VAL LEU ASN SEQRES 5 A 286 GLY LEU ILE TYR ALA VAL GLY GLY TYR ASP GLY ASN THR SEQRES 6 A 286 HIS LEU ASN SER VAL GLU ALA TYR ASP PRO HIS HIS ASN SEQRES 7 A 286 GLU TRP SER LEU VAL ALA PRO LEU SER THR ARG ARG SER SEQRES 8 A 286 GLY VAL GLY VAL ALA VAL LEU ASN GLY LEU ILE TYR ALA SEQRES 9 A 286 VAL GLY GLY TYR ASP GLY ASN THR HIS LEU ASN SER VAL SEQRES 10 A 286 GLU ALA TYR ASP PRO GLU ARG ASN GLU TRP SER LEU VAL SEQRES 11 A 286 ALA PRO LEU SER THR ARG ARG SER GLY VAL GLY VAL ALA SEQRES 12 A 286 VAL LEU ASN GLY LEU ILE TYR ALA VAL GLY GLY TYR ASP SEQRES 13 A 286 GLY ASN THR HIS LEU ASN SER VAL GLU ALA TYR ASP PRO SEQRES 14 A 286 HIS HIS ASN GLU TRP SER LEU VAL ALA PRO LEU SER THR SEQRES 15 A 286 ARG ARG SER GLY VAL GLY VAL ALA VAL LEU ASN GLY LEU SEQRES 16 A 286 ILE TYR ALA VAL GLY GLY TYR ASP GLY ASN THR HIS LEU SEQRES 17 A 286 ASN SER VAL GLU ALA TYR ASP PRO GLU ARG ASN GLU TRP SEQRES 18 A 286 SER LEU VAL ALA PRO LEU SER THR ARG ARG SER GLY VAL SEQRES 19 A 286 GLY VAL ALA VAL LEU ASN GLY LEU ILE TYR ALA VAL GLY SEQRES 20 A 286 GLY TYR ASP GLY ASN THR HIS LEU ASN SER VAL GLU ALA SEQRES 21 A 286 TYR ASP PRO HIS HIS ASN GLU TRP SER LEU VAL ALA PRO SEQRES 22 A 286 LEU SER THR ARG ARG SER GLY VAL GLY VAL ALA VAL LEU FORMUL 2 HOH *219(H2 O) SHEET 1 AA1 4 GLU A 32 LEU A 35 0 SHEET 2 AA1 4 HIS A 19 ASP A 27 -1 N ASP A 27 O GLU A 32 SHEET 3 AA1 4 ILE A 8 TYR A 14 -1 N ALA A 10 O GLU A 24 SHEET 4 AA1 4 GLY A 282 VAL A 285 -1 O ALA A 284 N TYR A 9 SHEET 1 AA2 4 GLY A 47 LEU A 51 0 SHEET 2 AA2 4 LEU A 54 TYR A 61 -1 O VAL A 58 N GLY A 47 SHEET 3 AA2 4 HIS A 66 ASP A 74 -1 O GLU A 71 N ALA A 57 SHEET 4 AA2 4 GLU A 79 LEU A 82 -1 O GLU A 79 N ASP A 74 SHEET 1 AA3 4 GLY A 94 LEU A 98 0 SHEET 2 AA3 4 LEU A 101 TYR A 108 -1 O TYR A 103 N ALA A 96 SHEET 3 AA3 4 HIS A 113 ASP A 121 -1 O GLU A 118 N ALA A 104 SHEET 4 AA3 4 GLU A 126 LEU A 129 -1 O GLU A 126 N ASP A 121 SHEET 1 AA4 4 GLY A 141 LEU A 145 0 SHEET 2 AA4 4 LEU A 148 TYR A 155 -1 O VAL A 152 N GLY A 141 SHEET 3 AA4 4 HIS A 160 ASP A 168 -1 O GLU A 165 N ALA A 151 SHEET 4 AA4 4 GLU A 173 LEU A 176 -1 O SER A 175 N ALA A 166 SHEET 1 AA5 4 GLY A 188 LEU A 192 0 SHEET 2 AA5 4 LEU A 195 TYR A 202 -1 O VAL A 199 N GLY A 188 SHEET 3 AA5 4 HIS A 207 ASP A 215 -1 O GLU A 212 N ALA A 198 SHEET 4 AA5 4 GLU A 220 LEU A 223 -1 O GLU A 220 N ASP A 215 SHEET 1 AA6 4 GLY A 235 LEU A 239 0 SHEET 2 AA6 4 LEU A 242 TYR A 249 -1 O TYR A 244 N ALA A 237 SHEET 3 AA6 4 HIS A 254 ASP A 262 -1 O GLU A 259 N ALA A 245 SHEET 4 AA6 4 GLU A 267 LEU A 270 -1 O GLU A 267 N ASP A 262 CRYST1 44.049 76.290 67.987 90.00 90.02 90.00 C 1 2 1 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 0.022702 0.000000 0.000008 0.00000 SCALE2 0.000000 0.013108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014709 0.00000