HEADER UNKNOWN FUNCTION 03-NOV-21 7Q58 TITLE CRYSTAL STRUCTURE OF THE SAKE6BR DESIGNER PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAKE6BR; 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,G.VELUPLA,D.E.CLARKE,A.R.D.VOET,S.DE FEYTER REVDAT 2 01-MAY-24 7Q58 1 REMARK REVDAT 1 22-FEB-23 7Q58 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 59908 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2941 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 28.3900 - 3.5900 1.00 2790 135 0.1469 0.1762 REMARK 3 2 3.5800 - 2.8500 1.00 2738 135 0.1574 0.1552 REMARK 3 3 2.8500 - 2.4900 1.00 2739 159 0.1474 0.1786 REMARK 3 4 2.4900 - 2.2600 1.00 2731 133 0.1469 0.1957 REMARK 3 5 2.2600 - 2.1000 1.00 2714 135 0.1308 0.1549 REMARK 3 6 2.1000 - 1.9700 1.00 2746 150 0.1321 0.1427 REMARK 3 7 1.9700 - 1.8700 1.00 2646 197 0.1268 0.1523 REMARK 3 8 1.8700 - 1.7900 1.00 2704 113 0.1298 0.1974 REMARK 3 9 1.7900 - 1.7200 1.00 2748 124 0.1262 0.1611 REMARK 3 10 1.7200 - 1.6600 1.00 2701 145 0.1289 0.1541 REMARK 3 11 1.6600 - 1.6100 1.00 2709 139 0.1398 0.1829 REMARK 3 12 1.6100 - 1.5700 1.00 2680 128 0.1388 0.1889 REMARK 3 13 1.5700 - 1.5300 1.00 2706 153 0.1380 0.1946 REMARK 3 14 1.5300 - 1.4900 1.00 2722 125 0.1339 0.2076 REMARK 3 15 1.4900 - 1.4500 1.00 2685 149 0.1336 0.1720 REMARK 3 16 1.4500 - 1.4200 1.00 2706 113 0.1393 0.1791 REMARK 3 17 1.4200 - 1.3900 1.00 2739 133 0.1500 0.2097 REMARK 3 18 1.3900 - 1.3700 1.00 2685 148 0.1736 0.1799 REMARK 3 19 1.3700 - 1.3400 1.00 2734 125 0.2143 0.2693 REMARK 3 20 1.3400 - 1.3200 1.00 2605 150 0.2472 0.2923 REMARK 3 21 1.3200 - 1.3000 1.00 2739 152 0.2860 0.3171 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.87 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 7Q58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-21 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88560 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59961 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 41.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.62800 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 2.8.3 REMARK 200 STARTING MODEL: DESIGNED MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 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 HANGING 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 25.16100 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 465 GLY A 1 REMARK 465 GLY A 2 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 GLU A 25 CD OE1 OE2 REMARK 470 GLU A 28 CD OE1 OE2 REMARK 470 GLU A 72 CD OE1 OE2 REMARK 470 GLU A 119 CD OE1 OE2 REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 GLU A 213 CD OE1 OE2 REMARK 470 GLU A 260 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 ASN A 13 -30.27 -130.02 REMARK 500 ASN A 60 -31.42 -130.50 REMARK 500 ASN A 201 -30.32 -131.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Q58 A -3 282 PDB 7Q58 7Q58 -3 282 SEQRES 1 A 286 GLY SER HIS MET GLY GLY LEU LEU TYR ALA VAL GLY GLY SEQRES 2 A 286 TYR ASP GLY ASN THR HIS LEU ASN SER LEU GLU CYS TYR SEQRES 3 A 286 ASN PRO GLU THR ASN GLU TRP SER PRO VAL ALA PRO LEU SEQRES 4 A 286 SER VAL PRO ARG SER GLY ILE GLY VAL ALA VAL LEU GLY SEQRES 5 A 286 GLY LEU LEU TYR ALA VAL GLY GLY TYR ASP GLY ASN THR SEQRES 6 A 286 HIS LEU ASN SER LEU GLU CYS TYR ASN PRO GLU THR ASN SEQRES 7 A 286 GLU TRP SER PRO VAL ALA PRO LEU SER VAL PRO ARG SER SEQRES 8 A 286 GLY ILE GLY VAL ALA VAL LEU GLY GLY LEU LEU TYR ALA SEQRES 9 A 286 VAL GLY GLY TYR ASP GLY ASN THR HIS LEU ASN SER LEU SEQRES 10 A 286 GLU CYS TYR ASN PRO GLU THR ASN GLU TRP SER PRO VAL SEQRES 11 A 286 ALA PRO LEU SER VAL PRO ARG SER GLY ILE GLY VAL ALA SEQRES 12 A 286 VAL LEU GLY GLY LEU LEU TYR ALA VAL GLY GLY TYR ASP SEQRES 13 A 286 GLY ASN THR HIS LEU ASN SER LEU GLU CYS TYR ASN PRO SEQRES 14 A 286 GLU THR ASN GLU TRP SER PRO VAL ALA PRO LEU SER VAL SEQRES 15 A 286 PRO ARG SER GLY ILE GLY VAL ALA VAL LEU GLY GLY LEU SEQRES 16 A 286 LEU TYR ALA VAL GLY GLY TYR ASP GLY ASN THR HIS LEU SEQRES 17 A 286 ASN SER LEU GLU CYS TYR ASN PRO GLU THR ASN GLU TRP SEQRES 18 A 286 SER PRO VAL ALA PRO LEU SER VAL PRO ARG SER GLY ILE SEQRES 19 A 286 GLY VAL ALA VAL LEU GLY GLY LEU LEU TYR ALA VAL GLY SEQRES 20 A 286 GLY TYR ASP GLY ASN THR HIS LEU ASN SER LEU GLU CYS SEQRES 21 A 286 TYR ASN PRO GLU THR ASN GLU TRP SER PRO VAL ALA PRO SEQRES 22 A 286 LEU SER VAL PRO ARG SER GLY ILE GLY VAL ALA VAL LEU FORMUL 2 HOH *306(H2 O) SHEET 1 AA1 4 GLU A 28 VAL A 32 0 SHEET 2 AA1 4 LEU A 19 ASN A 23 -1 N CYS A 21 O SER A 30 SHEET 3 AA1 4 LEU A 4 VAL A 7 -1 N ALA A 6 O GLU A 20 SHEET 4 AA1 4 GLY A 278 VAL A 281 -1 O ALA A 280 N TYR A 5 SHEET 1 AA2 4 GLY A 43 LEU A 47 0 SHEET 2 AA2 4 LEU A 50 VAL A 54 -1 O TYR A 52 N ALA A 45 SHEET 3 AA2 4 LEU A 66 ASN A 70 -1 O GLU A 67 N ALA A 53 SHEET 4 AA2 4 GLU A 75 PRO A 78 -1 O GLU A 75 N ASN A 70 SHEET 1 AA3 4 GLY A 90 LEU A 94 0 SHEET 2 AA3 4 LEU A 97 VAL A 101 -1 O TYR A 99 N ALA A 92 SHEET 3 AA3 4 LEU A 113 TYR A 116 -1 O GLU A 114 N ALA A 100 SHEET 4 AA3 4 TRP A 123 VAL A 126 -1 O SER A 124 N CYS A 115 SHEET 1 AA4 4 GLY A 137 LEU A 141 0 SHEET 2 AA4 4 LEU A 144 VAL A 148 -1 O TYR A 146 N ALA A 139 SHEET 3 AA4 4 LEU A 160 TYR A 163 -1 O GLU A 161 N ALA A 147 SHEET 4 AA4 4 TRP A 170 VAL A 173 -1 O SER A 171 N CYS A 162 SHEET 1 AA5 4 GLY A 184 LEU 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 LEU A 207 ASN A 211 -1 O GLU A 208 N ALA A 194 SHEET 4 AA5 4 GLU A 216 PRO A 219 -1 O GLU A 216 N ASN A 211 SHEET 1 AA6 4 GLY A 231 LEU A 235 0 SHEET 2 AA6 4 LEU A 238 VAL A 242 -1 O TYR A 240 N ALA A 233 SHEET 3 AA6 4 LEU A 254 ASN A 258 -1 O GLU A 255 N ALA A 241 SHEET 4 AA6 4 GLU A 263 VAL A 267 -1 O SER A 265 N CYS A 256 CRYST1 34.384 50.322 71.324 90.00 90.00 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 0.029083 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014021 0.00000 MASTER 246 0 0 0 24 0 0 6 2341 1 0 22 END