HEADER DE NOVO PROTEIN 05-MAY-23 8OYS TITLE DE NOVO DESIGNED TIM BARREL FOLD TBF_24 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED TIM-BARREL; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TIM BARREL, DE NOVO DESIGNED, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PACESA,B.E.CORREIA REVDAT 3 14-AUG-24 8OYS 1 JRNL REVDAT 2 27-MAR-24 8OYS 1 JRNL REVDAT 1 18-OCT-23 8OYS 0 JRNL AUTH C.A.GOVERDE,M.PACESA,N.GOLDBACH,L.J.DORNFELD,P.E.M.BALBI, JRNL AUTH 2 S.GEORGEON,S.ROSSET,S.KAPOOR,J.CHOUDHURY,J.DAUPARAS, JRNL AUTH 3 C.SCHELLHAAS,S.KOZLOV,D.BAKER,S.OVCHINNIKOV,A.J.VECCHIO, JRNL AUTH 4 B.E.CORREIA JRNL TITL COMPUTATIONAL DESIGN OF SOLUBLE AND FUNCTIONAL MEMBRANE JRNL TITL 2 PROTEIN ANALOGUES. JRNL REF NATURE V. 631 449 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38898281 JRNL DOI 10.1038/S41586-024-07601-Y REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.GOVERDE,M.PACESA,N.GOLDBACH,L.J.DORNFELD,P.E.M.BALBI, REMARK 1 AUTH 2 S.GEORGEON,S.ROSSET,S.KAPOOR,J.CHOUDHURY,J.DAUPARAS, REMARK 1 AUTH 3 C.SCHELLHAAS,S.KOZLOV,D.BAKER,S.OVCHINNIKOV,A.J.VECCHIO, REMARK 1 AUTH 4 B.E.CORREIA REMARK 1 TITL COMPUTATIONAL DESIGN OF SOLUBLE FUNCTIONAL ANALOGUES OF REMARK 1 TITL 2 INTEGRAL MEMBRANE PROTEINS. REMARK 1 REF BIORXIV 2024 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 38496615 REMARK 1 DOI 10.1101/2023.05.09.540044 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46891 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2383 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 62.7300 - 3.4500 0.99 2809 162 0.1742 0.1792 REMARK 3 2 3.4400 - 2.7300 1.00 2687 145 0.1740 0.1952 REMARK 3 3 2.7300 - 2.3900 1.00 2660 138 0.1594 0.1896 REMARK 3 4 2.3900 - 2.1700 1.00 2630 162 0.1464 0.1649 REMARK 3 5 2.1700 - 2.0100 1.00 2618 143 0.1457 0.1724 REMARK 3 6 2.0100 - 1.9000 1.00 2627 142 0.1601 0.1900 REMARK 3 7 1.9000 - 1.8000 1.00 2602 140 0.1471 0.2041 REMARK 3 8 1.8000 - 1.7200 1.00 2595 145 0.1396 0.1758 REMARK 3 9 1.7200 - 1.6600 1.00 2596 140 0.1436 0.1888 REMARK 3 10 1.6600 - 1.6000 1.00 2573 136 0.1531 0.1955 REMARK 3 11 1.6000 - 1.5500 0.99 2597 142 0.1752 0.2077 REMARK 3 12 1.5500 - 1.5000 1.00 2601 128 0.1788 0.2168 REMARK 3 13 1.5000 - 1.4700 1.00 2562 139 0.1774 0.2259 REMARK 3 14 1.4700 - 1.4300 1.00 2620 122 0.2049 0.2066 REMARK 3 15 1.4300 - 1.4000 1.00 2575 137 0.2260 0.2978 REMARK 3 16 1.4000 - 1.3700 1.00 2594 119 0.2631 0.2724 REMARK 3 17 1.3700 - 1.3400 1.00 2562 143 0.3035 0.3509 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 20.978 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.06 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 1405 REMARK 3 ANGLE : 0.838 1901 REMARK 3 CHIRALITY : 0.066 237 REMARK 3 PLANARITY : 0.005 239 REMARK 3 DIHEDRAL : 12.484 531 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 8OYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46891 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 62.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.05821 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 1.42200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.380 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA3 CIT, 1 M LICL, 20% PEG 6K, REMARK 280 PH 4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K 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 18.31450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.72950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.20350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.72950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.31450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.20350 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 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 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 MET A 0 N CA CB CG SD CE REMARK 470 GLY A 189 CA C O 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 LYS A 65 -77.26 -98.04 REMARK 500 ASP A 141 -39.65 68.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 8OYS A 0 189 PDB 8OYS 8OYS 0 189 SEQRES 1 A 190 MET SER THR ILE GLU GLU LEU ILE LYS ALA ALA LYS GLU SEQRES 2 A 190 LEU LYS SER LEU GLY ILE GLU ASN ILE ILE ILE GLU VAL SEQRES 3 A 190 LYS SER ALA GLU ASP ALA LYS LYS ILE ALA ALA GLU GLY SEQRES 4 A 190 PHE GLU LYS ILE LEU VAL SER GLY PRO LYS THR GLU GLU SEQRES 5 A 190 GLY ILE ALA MET ALA ALA ALA ALA LYS ALA ALA GLY ALA SEQRES 6 A 190 LYS ASN ILE ILE VAL THR ALA ARG THR ALA GLU GLU ALA SEQRES 7 A 190 LEU ALA ALA LEU ALA THR PRO GLY VAL THR GLY VAL LEU SEQRES 8 A 190 LEU THR THR THR ALA GLU GLU ALA PRO ALA ALA LEU ALA SEQRES 9 A 190 THR LEU LYS ALA ALA GLY TYR THR ASN VAL ILE PHE ARG SEQRES 10 A 190 GLY PRO SER ILE GLU GLU VAL LYS LYS MET ILE GLU TYR SEQRES 11 A 190 GLY ALA GLU LYS VAL LEU ILE SER SER LYS ASP ASP GLU SEQRES 12 A 190 GLU ALA ILE LYS ALA ALA ALA GLU LEU LYS ALA LYS GLY SEQRES 13 A 190 VAL LYS ASN ILE ILE VAL ALA THR ARG ASP ILE GLU ALA SEQRES 14 A 190 ALA LYS LYS ALA TYR GLU ALA GLY ALA SER SER ILE LEU SEQRES 15 A 190 LEU VAL PRO ASP GLY SER TRP GLY HET CL A 201 1 HET CL A 202 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *232(H2 O) HELIX 1 AA1 THR A 2 LEU A 16 1 15 HELIX 2 AA2 SER A 27 GLU A 37 1 11 HELIX 3 AA3 LYS A 48 ALA A 62 1 15 HELIX 4 AA4 THR A 73 ALA A 82 1 10 HELIX 5 AA5 GLU A 97 GLY A 109 1 13 HELIX 6 AA6 SER A 119 GLY A 130 1 12 HELIX 7 AA7 ASP A 141 LYS A 154 1 14 HELIX 8 AA8 ASP A 165 ALA A 175 1 11 SHEET 1 AA1 9 ILE A 21 VAL A 25 0 SHEET 2 AA1 9 LYS A 41 VAL A 44 1 O LEU A 43 N VAL A 25 SHEET 3 AA1 9 ASN A 66 ALA A 71 1 O ILE A 68 N ILE A 42 SHEET 4 AA1 9 GLY A 88 THR A 92 1 O THR A 92 N ALA A 71 SHEET 5 AA1 9 VAL A 113 ARG A 116 1 O ILE A 114 N VAL A 89 SHEET 6 AA1 9 LYS A 133 ILE A 136 1 O LYS A 133 N PHE A 115 SHEET 7 AA1 9 ILE A 159 THR A 163 1 O ILE A 160 N VAL A 134 SHEET 8 AA1 9 SER A 179 LEU A 182 1 O LEU A 181 N THR A 163 SHEET 9 AA1 9 ILE A 21 VAL A 25 1 N ILE A 22 O LEU A 182 CRYST1 36.629 44.407 125.459 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 0.027301 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022519 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007971 0.00000