HEADER DE NOVO PROTEIN 09-JUN-21 7OSV TITLE DENOVOTIM6-SB, A DE NOVO DESIGNED TIM BARREL WITH A SALT-BRIDGE TITLE 2 CLUSTER (CRYSTAL FORM 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DENOVOTIM6-SB; 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: PET21B(+) KEYWDS TIM BARREL, SALT BRIDGE CLUSTER, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KORDES,S.ROMERO-ROMERO,B.HOCKER REVDAT 3 31-JAN-24 7OSV 1 REMARK REVDAT 2 16-FEB-22 7OSV 1 JRNL REVDAT 1 15-DEC-21 7OSV 0 JRNL AUTH S.KORDES,S.ROMERO-ROMERO,L.LUTZ,B.HOCKER JRNL TITL A NEWLY INTRODUCED SALT BRIDGE CLUSTER IMPROVES STRUCTURAL JRNL TITL 2 AND BIOPHYSICAL PROPERTIES OF DE NOVO TIM BARRELS. JRNL REF PROTEIN SCI. V. 31 513 2022 JRNL REFN ESSN 1469-896X JRNL PMID 34865275 JRNL DOI 10.1002/PRO.4249 REMARK 2 REMARK 2 RESOLUTION. 1.66 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 19751 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 988 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 32.8100 - 3.1700 0.99 2719 144 0.1865 0.2131 REMARK 3 2 3.1700 - 2.5200 1.00 2727 143 0.2128 0.2366 REMARK 3 3 2.5200 - 2.2000 1.00 2700 143 0.1927 0.2395 REMARK 3 4 2.2000 - 2.0000 0.98 2664 140 0.1973 0.2204 REMARK 3 5 2.0000 - 1.8500 0.99 2672 140 0.2521 0.3067 REMARK 3 6 1.8500 - 1.7500 0.99 2685 141 0.2990 0.3151 REMARK 3 7 1.7500 - 1.6600 0.96 2596 137 0.3767 0.3713 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) : 0.268 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.689 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.70 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 : 0.006 1390 REMARK 3 ANGLE : 0.592 1876 REMARK 3 CHIRALITY : 0.049 212 REMARK 3 PLANARITY : 0.005 244 REMARK 3 DIHEDRAL : 6.930 196 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): 17.9931 23.1376 32.2013 REMARK 3 T TENSOR REMARK 3 T11: 0.2128 T22: 0.2166 REMARK 3 T33: 0.2395 T12: 0.0052 REMARK 3 T13: -0.0202 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 1.3013 L22: 2.2167 REMARK 3 L33: 0.5303 L12: -0.2505 REMARK 3 L13: -0.3257 L23: 0.0699 REMARK 3 S TENSOR REMARK 3 S11: 0.0311 S12: 0.0230 S13: 0.0207 REMARK 3 S21: 0.0719 S22: -0.0372 S23: -0.0068 REMARK 3 S31: -0.0258 S32: -0.0434 S33: 0.0196 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 7OSV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 1.0 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19751 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 32.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.13850 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.77000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.960 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: 5BVL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.2 M SODIUM REMARK 280 ACETATE PH 4.6, 28% PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 32.81500 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 TOTAL BURIED SURFACE AREA: 640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8610 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 1 REMARK 465 ASP A 2 REMARK 465 LYS A 3 REMARK 465 ASP A 4 REMARK 465 GLU A 5 REMARK 465 ALA A 6 REMARK 465 TRP A 7 REMARK 465 LYS A 95 REMARK 465 ASP A 96 REMARK 465 GLU A 97 REMARK 465 ALA A 98 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 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 LYS A 8 CG CD CE NZ REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 19 CD CE NZ REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 LYS A 54 CD CE NZ REMARK 470 ARG A 61 CZ NH1 NH2 REMARK 470 LYS A 65 CD CE NZ REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 LYS A 83 CE NZ REMARK 470 THR A 93 OG1 CG2 REMARK 470 ASP A 94 CG OD1 OD2 REMARK 470 TRP A 99 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 99 CZ3 CH2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 ARG A 116 NE CZ NH1 NH2 REMARK 470 LYS A 129 CD CE NZ REMARK 470 LYS A 174 CD CE NZ 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 415 DISTANCE = 6.28 ANGSTROMS DBREF 7OSV A 1 194 PDB 7OSV 7OSV 1 194 SEQRES 1 A 194 MET ASP LYS ASP GLU ALA TRP LYS GLN VAL GLU ILE LEU SEQRES 2 A 194 ARG ARG LEU GLY ALA LYS ARG ILE ALA TYR ARG SER ASP SEQRES 3 A 194 ASP TRP ARG ASP LEU GLN GLU ALA LEU LYS LYS GLY ALA SEQRES 4 A 194 ASP ILE LEU ILE VAL ASP ALA THR ASP LYS ASP GLU ALA SEQRES 5 A 194 TRP LYS GLN VAL GLU ILE LEU ARG ARG LEU GLY ALA LYS SEQRES 6 A 194 GLU ILE ALA TYR ARG SER ASP ASP TRP ARG ASP LEU GLN SEQRES 7 A 194 GLU ALA LEU LYS LYS GLY ALA ASP ILE LEU ILE VAL ASP SEQRES 8 A 194 ALA THR ASP LYS ASP GLU ALA TRP LYS GLN VAL GLU ILE SEQRES 9 A 194 LEU ARG ARG LEU GLY ALA LYS ARG ILE ALA TYR ARG SER SEQRES 10 A 194 ASP ASP TRP ARG ASP LEU GLN GLU ALA LEU LYS LYS GLY SEQRES 11 A 194 ALA ASP ILE LEU ILE VAL ASP ALA THR ASP LYS ASP GLU SEQRES 12 A 194 ALA TRP LYS GLN VAL GLU ILE LEU ARG ARG LEU GLY ALA SEQRES 13 A 194 LYS GLU ILE ALA TYR ARG SER ASP ASP TRP ARG ASP LEU SEQRES 14 A 194 GLN GLU ALA LEU LYS LYS GLY ALA ASP ILE LEU ILE VAL SEQRES 15 A 194 ASP ALA THR GLY LEU GLU HIS HIS HIS HIS HIS HIS HET SO4 A 201 5 HET ACT A 202 7 HET ACT A 203 7 HET PEG A 204 17 HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 SO4 O4 S 2- FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *115(H2 O) HELIX 1 AA1 LYS A 8 GLY A 17 1 10 HELIX 2 AA2 ASP A 27 LYS A 37 1 11 HELIX 3 AA3 ALA A 52 LEU A 62 1 11 HELIX 4 AA4 ASP A 73 GLY A 84 1 12 HELIX 5 AA5 LYS A 100 GLY A 109 1 10 HELIX 6 AA6 ASP A 119 LYS A 129 1 11 HELIX 7 AA7 ALA A 144 LEU A 154 1 11 HELIX 8 AA8 ASP A 165 LYS A 175 1 11 SHEET 1 AA1 9 ARG A 20 SER A 25 0 SHEET 2 AA1 9 ILE A 41 ASP A 45 1 O ILE A 43 N TYR A 23 SHEET 3 AA1 9 ILE A 67 ARG A 70 1 O ALA A 68 N LEU A 42 SHEET 4 AA1 9 ILE A 87 ASP A 91 1 O ILE A 89 N TYR A 69 SHEET 5 AA1 9 ARG A 112 SER A 117 1 O ALA A 114 N LEU A 88 SHEET 6 AA1 9 ILE A 133 ASP A 137 1 O ILE A 135 N TYR 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 TYR A 161 SHEET 9 AA1 9 ARG A 20 SER A 25 1 N ALA A 22 O LEU A 180 CRYST1 29.370 65.630 44.610 90.00 95.74 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 0.034048 0.000000 0.003421 0.00000 SCALE2 0.000000 0.015237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022529 0.00000