HEADER DE NOVO PROTEIN 18-APR-20 6YQX TITLE CRYSTAL STRUCTURE OF DENOVOTIM13, A DE NOVO DESIGNED TIM BARREL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED TIM BARREL DENOVOTIM13; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: M (N-TERMINAL) AND GLEHHHHHH (C-TERMINAL) COME FROM COMPND 6 THE EXPRESION VECTOR. 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: PET29B(+) KEYWDS DE NOVO PROTEIN DESIGN, EPISTASIS, STABILITY LANDSCAPE, TIM BARREL, KEYWDS 2 (BETA/ALFA)8 BARREL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ROMERO-ROMERO,S.KORDES,S.SHANMUGARATNAM,D.A.FERNANDEZ-VELASCO, AUTHOR 2 B.HOCKER REVDAT 4 01-MAY-24 6YQX 1 REMARK REVDAT 3 04-AUG-21 6YQX 1 JRNL REVDAT 2 28-JUL-21 6YQX 1 JRNL REVDAT 1 21-JUL-21 6YQX 0 JRNL AUTH S.ROMERO-ROMERO,M.COSTAS,D.A.SILVA MANZANO,S.KORDES, JRNL AUTH 2 E.ROJAS-ORTEGA,C.TAPIA,Y.GUERRA,S.SHANMUGARATNAM, JRNL AUTH 3 A.RODRIGUEZ-ROMERO,D.BAKER,B.HOCKER,D.A.FERNANDEZ-VELASCO JRNL TITL THE STABILITY LANDSCAPE OF DE NOVO TIM BARRELS EXPLORED BY A JRNL TITL 2 MODULAR DESIGN APPROACH. JRNL REF J.MOL.BIOL. V. 433 67153 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 34271011 JRNL DOI 10.1016/J.JMB.2021.167153 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 23405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.470 REMARK 3 FREE R VALUE TEST SET COUNT : 1983 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 10.0000 - 3.9480 0.99 1525 133 0.1528 0.1541 REMARK 3 2 3.9480 - 3.1339 0.99 1546 136 0.1473 0.2122 REMARK 3 3 3.1339 - 2.7378 1.00 1520 135 0.1819 0.2051 REMARK 3 4 2.7378 - 2.4875 1.00 1540 143 0.1722 0.2196 REMARK 3 5 2.4875 - 2.3092 0.99 1544 148 0.1768 0.2045 REMARK 3 6 2.3092 - 2.1731 0.99 1512 144 0.1688 0.1859 REMARK 3 7 2.1731 - 2.0642 1.00 1528 142 0.1745 0.2051 REMARK 3 8 2.0642 - 1.9744 1.00 1554 146 0.1920 0.2259 REMARK 3 9 1.9744 - 1.8984 1.00 1527 140 0.1977 0.2386 REMARK 3 10 1.8984 - 1.8329 1.00 1525 146 0.2080 0.2584 REMARK 3 11 1.8329 - 1.7756 1.00 1521 139 0.2197 0.2568 REMARK 3 12 1.7756 - 1.7248 1.00 1553 140 0.2347 0.2745 REMARK 3 13 1.7248 - 1.6794 1.00 1539 145 0.2648 0.2717 REMARK 3 14 1.6794 - 1.6384 0.97 1488 146 0.2739 0.3269 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 20.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.21 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: (CHAIN A AND RESSEQ 2:184) REMARK 3 ORIGIN FOR THE GROUP (A): 4.2974 16.4939 -2.6164 REMARK 3 T TENSOR REMARK 3 T11: 0.1724 T22: 0.1631 REMARK 3 T33: 0.1804 T12: -0.0370 REMARK 3 T13: 0.0167 T23: 0.0297 REMARK 3 L TENSOR REMARK 3 L11: 2.1456 L22: 2.9797 REMARK 3 L33: 2.5679 L12: -0.8906 REMARK 3 L13: -0.1374 L23: 1.0604 REMARK 3 S TENSOR REMARK 3 S11: 0.0262 S12: -0.0605 S13: -0.2594 REMARK 3 S21: 0.1231 S22: -0.1149 S23: 0.1501 REMARK 3 S31: 0.1907 S32: -0.1388 S33: 0.0595 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 6YQX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23407 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.638 REMARK 200 RESOLUTION RANGE LOW (A) : 44.793 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.55200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.15_3459 REMARK 200 STARTING MODEL: ROSETTA BACKBONE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M SODIUM ACETATE, 0.085 M TRIS REMARK 280 PH: 8.5, 25% W/V PEG 4000, 15% V/V GLYCEROL., PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,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 42.64533 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 21.32267 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: 350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 1 REMARK 465 ALA A 46 REMARK 465 THR A 47 REMARK 465 THR A 185 REMARK 465 GLY A 186 REMARK 465 LEU A 187 REMARK 465 GLU A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 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 425 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 426 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 427 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A 429 DISTANCE = 7.87 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 DBREF 6YQX A 1 194 PDB 6YQX 6YQX 1 194 SEQRES 1 A 194 MET ASP VAL ASP GLU MET LEU LYS GLN VAL GLU ILE LEU SEQRES 2 A 194 ARG ARG LEU GLY ALA LYS GLN ILE ALA VAL ARG SER ASP SEQRES 3 A 194 ASP TRP ARG ILE LEU GLN GLU ALA LEU LYS LYS GLY GLY SEQRES 4 A 194 ASP ILE LEU ILE VAL ASP ALA THR ASP VAL ASP GLU MET SEQRES 5 A 194 LEU LYS GLN VAL GLU ILE LEU ARG ARG LEU GLY ALA LYS SEQRES 6 A 194 GLN ILE ALA VAL ARG SER ASP ASP TRP ARG ILE LEU GLN SEQRES 7 A 194 GLU ALA LEU LYS LYS GLY GLY ASP ILE LEU ILE VAL ASP SEQRES 8 A 194 ALA THR ASP VAL ASP GLU MET LEU LYS GLN VAL GLU ILE SEQRES 9 A 194 LEU ARG ARG LEU GLY ALA LYS GLN ILE ALA VAL ARG SER SEQRES 10 A 194 ASP ASP TRP ARG ILE LEU GLN GLU ALA LEU LYS LYS GLY SEQRES 11 A 194 GLY ASP ILE LEU ILE VAL ASP ALA THR ASP VAL ASP GLU SEQRES 12 A 194 MET LEU LYS GLN VAL GLU ILE LEU ARG ARG LEU GLY ALA SEQRES 13 A 194 LYS GLN ILE ALA VAL ARG SER ASP ASP TRP ARG ILE LEU SEQRES 14 A 194 GLN GLU ALA LEU LYS LYS GLY GLY ASP ILE LEU ILE VAL SEQRES 15 A 194 ASP ALA THR GLY LEU GLU HIS HIS HIS HIS HIS HIS HET GOL A 201 6 HET CL A 202 1 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 CL CL 1- FORMUL 4 HOH *128(H2 O) HELIX 1 AA1 ASP A 2 LEU A 16 1 15 HELIX 2 AA2 ASP A 27 GLY A 38 1 12 HELIX 3 AA3 VAL A 49 LEU A 62 1 14 HELIX 4 AA4 ASP A 73 LYS A 83 1 11 HELIX 5 AA5 ASP A 94 LEU A 108 1 15 HELIX 6 AA6 ASP A 119 GLY A 130 1 12 HELIX 7 AA7 ASP A 140 LEU A 154 1 15 HELIX 8 AA8 ASP A 165 GLY A 176 1 12 SHEET 1 AA1 9 GLN A 20 SER A 25 0 SHEET 2 AA1 9 ILE A 41 VAL A 44 1 O ILE A 43 N VAL A 23 SHEET 3 AA1 9 ILE A 67 SER A 71 1 O ALA A 68 N VAL A 44 SHEET 4 AA1 9 ILE A 87 ASP A 91 1 O ILE A 89 N VAL A 69 SHEET 5 AA1 9 ILE A 113 SER A 117 1 O ALA A 114 N VAL A 90 SHEET 6 AA1 9 ILE A 133 ASP A 137 1 O ILE A 135 N VAL A 115 SHEET 7 AA1 9 ILE A 159 ARG A 162 1 O ALA A 160 N LEU A 134 SHEET 8 AA1 9 ILE A 179 ASP A 183 1 O ILE A 181 N VAL A 161 SHEET 9 AA1 9 GLN A 20 SER A 25 1 N ALA A 22 O VAL A 182 SITE 1 AC1 9 GLU A 5 LYS A 8 GLN A 9 ILE A 12 SITE 2 AC1 9 LYS A 111 ASP A 132 TRP A 166 HOH A 355 SITE 3 AC1 9 HOH A 412 SITE 1 AC2 2 ARG A 24 ARG A 116 CRYST1 51.722 51.722 63.968 90.00 90.00 120.00 P 32 3 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 0.019334 0.011163 0.000000 0.00000 SCALE2 0.000000 0.022325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015633 0.00000