HEADER DE NOVO PROTEIN 21-MAR-22 7UEK TITLE CRYSTAL STRUCTURE OF A DE NOVO DESIGNED OVOID TIM BARREL OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OT3; 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 KEYWDS TIM BARREL, DE NOVO, OVAL CURVATURE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.E.CHU,D.FERNANDEZ,P.-S.HUANG REVDAT 3 03-APR-24 7UEK 1 REMARK REVDAT 2 01-NOV-23 7UEK 1 JRNL REVDAT 1 18-JAN-23 7UEK 0 JRNL AUTH A.E.CHU,D.FERNANDEZ,J.LIU,R.R.EGUCHI,P.S.HUANG JRNL TITL DE NOVO DESIGN OF A HIGHLY STABLE OVOID TIM BARREL: JRNL TITL 2 UNLOCKING POCKET SHAPE TOWARDS FUNCTIONAL DESIGN. JRNL REF BIODES RES V.2022 42315 2022 JRNL REFN ESSN 2693-1257 JRNL PMID 37850141 JRNL DOI 10.34133/2022/9842315 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 13666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 685 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 38.8430 - 4.5223 0.97 1371 83 0.2095 0.1978 REMARK 3 2 4.5223 - 3.5903 0.98 1319 71 0.1940 0.2119 REMARK 3 3 3.5903 - 3.1367 0.99 1324 66 0.2174 0.2898 REMARK 3 4 3.1367 - 2.8500 0.99 1276 69 0.2651 0.3752 REMARK 3 5 2.8500 - 2.6458 0.99 1292 66 0.2384 0.2569 REMARK 3 6 2.6458 - 2.4898 0.98 1281 80 0.2477 0.2672 REMARK 3 7 2.4898 - 2.3651 0.98 1264 65 0.2586 0.3168 REMARK 3 8 2.3651 - 2.2622 0.98 1289 61 0.2684 0.3562 REMARK 3 9 2.2622 - 2.1751 0.98 1295 61 0.2871 0.3388 REMARK 3 10 2.1751 - 2.1001 0.99 1270 63 0.3207 0.3329 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.87 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 4.9297 0.2408 -9.9014 REMARK 3 T TENSOR REMARK 3 T11: 0.2321 T22: 0.2220 REMARK 3 T33: 0.3764 T12: -0.0127 REMARK 3 T13: -0.0468 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 3.2564 L22: 5.1054 REMARK 3 L33: 1.6989 L12: -0.6238 REMARK 3 L13: -0.3034 L23: 0.5393 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: -0.0436 S13: 0.2739 REMARK 3 S21: -0.0158 S22: 0.0370 S23: -0.0924 REMARK 3 S31: -0.0889 S32: 0.0725 S33: -0.0148 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 7UEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000262732. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13666 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.843 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 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: COMPUTATIONAL DESIGN REMARK 200 REMARK 200 REMARK: 100S UM STRAIGHT ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BUFFER: 20 MM TRIS, 150 MM SODIUM REMARK 280 CHLORIDE, PH 8.0. SCREEN: 0.3 M MAGNESIUM CHLORIDE, 0.3 M REMARK 280 CALCIUM CHLORIDE, 1 M TRIS BICINE, 10% PEG8000, 25% ETHYLENE REMARK 280 GLYCOL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 305K 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 22.42400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.84300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.76300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.84300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.42400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.76300 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: 11410 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 MET A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 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 GLU A 9 -13.21 51.42 REMARK 500 ALA A 54 77.32 -102.33 REMARK 500 THR A 97 -130.53 39.87 REMARK 500 THR A 211 -80.54 -124.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UEK A -13 228 PDB 7UEK 7UEK -13 228 SEQRES 1 A 242 MET HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SEQRES 2 A 242 SER ASP ALA ILE CYS ILE TYR LEU ASP GLU SER ALA THR SEQRES 3 A 242 TRP LYS ASP MET LYS LYS ALA MET GLU ILE LEU TYR LYS SEQRES 4 A 242 LEU GLY VAL LYS LYS ILE VAL VAL LEU PHE LYS TYR ASP SEQRES 5 A 242 GLU LYS LEU ILE LYS VAL ALA ALA LYS VAL LEU HIS ASP SEQRES 6 A 242 LEU GLY ALA GLU GLU ALA ILE ILE ILE LEU ILE PHE ASP SEQRES 7 A 242 ILE ASP ASP GLU ASP GLU PHE LYS LYS GLN VAL LYS LYS SEQRES 8 A 242 ALA LEU GLU LEU MET LYS LYS LEU GLY VAL ASP HIS ARG SEQRES 9 A 242 ILE ILE ALA LEU ARG MET THR ASP GLU GLU LYS PHE LYS SEQRES 10 A 242 LYS LEU ALA LYS ILE ALA ALA GLU LEU GLY ALA ASP ALA SEQRES 11 A 242 ILE CYS ILE TYR LEU ASP GLU SER ALA THR TRP LYS ASP SEQRES 12 A 242 MET LYS LYS ALA MET GLU ILE LEU TYR LYS LEU GLY VAL SEQRES 13 A 242 LYS LYS ILE VAL VAL LEU PHE LYS TYR ASP GLU LYS LEU SEQRES 14 A 242 ILE LYS VAL ALA ALA LYS VAL LEU HIS ASP LEU GLY ALA SEQRES 15 A 242 GLU GLU ALA ILE ILE ILE LEU ILE PHE ASP ILE ASP ASP SEQRES 16 A 242 GLU ASP GLU PHE LYS LYS GLN VAL LYS LYS ALA LEU GLU SEQRES 17 A 242 LEU MET LYS LYS LEU GLY VAL ASP HIS ARG ILE ILE ALA SEQRES 18 A 242 LEU ARG MET THR ASP GLU GLU LYS PHE LYS LYS LEU ALA SEQRES 19 A 242 LYS ILE ALA ALA GLU LEU GLY ALA FORMUL 2 HOH *30(H2 O) HELIX 1 AA1 THR A 12 GLY A 27 1 16 HELIX 2 AA2 ASP A 38 GLY A 53 1 16 HELIX 3 AA3 ASP A 67 LEU A 85 1 19 HELIX 4 AA4 ASP A 98 GLY A 113 1 16 HELIX 5 AA5 THR A 126 GLY A 141 1 16 HELIX 6 AA6 ASP A 152 GLY A 167 1 16 HELIX 7 AA7 ASP A 181 LEU A 199 1 19 HELIX 8 AA8 ASP A 212 GLY A 227 1 16 SHEET 1 AA1 9 ALA A 2 LEU A 7 0 SHEET 2 AA1 9 ILE A 31 LYS A 36 1 O VAL A 32 N ILE A 5 SHEET 3 AA1 9 ILE A 58 PHE A 63 1 O ILE A 60 N VAL A 33 SHEET 4 AA1 9 ARG A 90 ARG A 95 1 O ALA A 93 N LEU A 61 SHEET 5 AA1 9 ALA A 116 TYR A 120 1 O CYS A 118 N LEU A 94 SHEET 6 AA1 9 ILE A 145 LYS A 150 1 O VAL A 146 N ILE A 119 SHEET 7 AA1 9 ILE A 172 ILE A 176 1 O ILE A 174 N VAL A 147 SHEET 8 AA1 9 ARG A 204 MET A 210 1 O ALA A 207 N LEU A 175 SHEET 9 AA1 9 ALA A 2 LEU A 7 1 N CYS A 4 O LEU A 208 CRYST1 44.848 65.526 77.686 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 0.022298 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012872 0.00000