HEADER DE NOVO PROTEIN 21-JUL-25 9S1T TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED SIX-HELIX BARREL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED HELICAL BARREL - 6H5L; 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 PARAMETRIC DESIGN, DE NOVO DESIGN, HELIX BARREL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.OBERDORFER,W.ELAILY,D.STOLL,M.CHAKATOK,B.GRILL REVDAT 1 29-JUL-26 9S1T 0 JRNL AUTH W.ELAILY,D.STOLL,M.CHAKATOK,M.ALEOTTI,B.GRILL,H.LECHNER, JRNL AUTH 2 G.OBERDORFER JRNL TITL DE NOVO DESIGN OF A THERMOSTABLE HELICAL BARREL PROTEIN FOR JRNL TITL 2 RAPID BIOCATALYTIC FUNCTIONALIZATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 7353 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.269 REMARK 3 R VALUE (WORKING SET) : 0.263 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 739 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 36.9100 - 4.7800 0.93 1285 144 0.2993 0.3131 REMARK 3 2 4.7800 - 3.8000 0.97 1318 149 0.2340 0.3064 REMARK 3 3 3.8000 - 3.3200 0.97 1342 151 0.2522 0.3495 REMARK 3 4 3.3200 - 3.0100 0.98 1354 149 0.2726 0.3179 REMARK 3 5 3.0100 - 2.8000 0.97 1315 146 0.2542 0.3248 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) : 0.317 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.52 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 : 0.001 2355 REMARK 3 ANGLE : 0.273 3119 REMARK 3 CHIRALITY : 0.027 385 REMARK 3 PLANARITY : 0.001 370 REMARK 3 DIHEDRAL : 10.161 985 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 9S1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1292149573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14388 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.01 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11000 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: NULL REMARK 200 REMARK 200 REMARK: LARGE PLATE-LIKE SHARD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17.5% PEG 3350, PH = 7.8, 150 MM L REMARK 280 -MALIC ACID, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 MET A -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 GLU A -9 REMARK 465 ASN A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 PHE A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLU A 49 REMARK 465 LYS A 50 REMARK 465 GLY A 51 REMARK 465 LEU A 52 REMARK 465 ASP A 53 REMARK 465 THR A 54 REMARK 465 LYS A 55 REMARK 465 GLU A 151 REMARK 465 LYS A 152 REMARK 465 GLY A 153 REMARK 465 LEU A 154 REMARK 465 ASP A 155 REMARK 465 THR A 156 REMARK 465 LYS A 157 REMARK 465 TYR A 254 REMARK 465 GLY A 255 REMARK 465 LEU A 256 REMARK 465 ASP A 257 REMARK 465 THR A 258 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 ALA A 90 -53.14 63.44 REMARK 500 GLN A 304 68.89 -105.12 REMARK 500 CYS A 305 48.42 -76.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 9S1T A -22 306 PDB 9S1T 9S1T -22 306 SEQRES 1 A 329 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 329 GLU ASN LEU TYR PHE GLN GLY SER HIS MET THR CYS GLU SEQRES 3 A 329 VAL VAL LYS LYS ILE LEU TYR MET ALA LYS LYS LEU VAL SEQRES 4 A 329 GLU GLN LYS LYS GLU VAL VAL LYS GLN ILE LEU LYS MET SEQRES 5 A 329 ALA LYS GLU LEU VAL GLU LYS LYS LYS GLU VAL VAL TYR SEQRES 6 A 329 LYS ALA LEU GLU ALA ALA GLU LYS GLY LEU ASP THR LYS SEQRES 7 A 329 LYS ILE ALA LYS LEU LEU LEU GLU MET LEU GLU HIS GLU SEQRES 8 A 329 LEU GLU LEU ALA GLU GLN ILE ALA LYS LEU LEU LEU GLU SEQRES 9 A 329 MET LEU GLU GLU GLU LEU GLN LEU ALA GLU LYS ILE ALA SEQRES 10 A 329 GLN LEU MET LEU GLU SER GLY ILE SER GLU GLU VAL VAL SEQRES 11 A 329 LYS GLN ILE LEU TYR MET ALA LYS GLN LEU VAL GLU LYS SEQRES 12 A 329 LYS LYS GLU VAL VAL LYS LYS ILE LEU TYR MET ALA LYS SEQRES 13 A 329 GLU LEU VAL GLU LYS LYS LYS GLU VAL VAL GLN LYS ALA SEQRES 14 A 329 LEU GLU ALA ALA GLU LYS GLY LEU ASP THR LYS GLN ILE SEQRES 15 A 329 ALA LYS LEU LEU LEU GLU MET LEU GLU HIS GLU LEU GLU SEQRES 16 A 329 LEU ALA GLU LYS ILE ALA GLN LEU LEU LEU GLU MET LEU SEQRES 17 A 329 GLU GLU GLU LEU LYS LEU ALA GLU LYS ILE ALA LYS LEU SEQRES 18 A 329 MET LEU GLU SER GLY ILE SER GLU GLU VAL VAL LYS LYS SEQRES 19 A 329 ILE LEU GLN MET ALA LYS LYS LEU VAL GLU LYS LYS LYS SEQRES 20 A 329 GLU VAL VAL GLN LYS ILE LEU TYR MET ALA GLN GLU LEU SEQRES 21 A 329 VAL GLU LYS LYS GLN GLU VAL VAL LYS LYS ALA LEU GLU SEQRES 22 A 329 ALA ALA GLU TYR GLY LEU ASP THR LYS LYS ILE ALA GLN SEQRES 23 A 329 LEU LEU LEU GLU MET LEU GLU HIS GLU LEU GLU LEU ALA SEQRES 24 A 329 GLU LYS ILE ALA LYS LEU LEU LEU GLU MET LEU GLU GLU SEQRES 25 A 329 GLU LEU LYS LEU ALA GLU LYS ILE ALA LYS LEU MET GLU SEQRES 26 A 329 GLU GLN CYS LYS HET LMR A 401 9 HET LMR A 402 9 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET PO4 A 406 5 HETNAM LMR (2S)-2-HYDROXYBUTANEDIOIC ACID HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN LMR L-MALATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 LMR 2(C4 H6 O5) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *29(H2 O) HELIX 1 AA1 GLU A 3 ALA A 44 1 42 HELIX 2 AA2 ILE A 57 SER A 100 1 44 HELIX 3 AA3 SER A 103 ALA A 149 1 47 HELIX 4 AA4 ILE A 159 SER A 202 1 44 HELIX 5 AA5 SER A 205 ALA A 252 1 48 HELIX 6 AA6 LYS A 260 GLN A 304 1 45 SSBOND 1 CYS A 2 CYS A 305 1555 1555 2.03 CRYST1 36.567 38.600 59.452 101.11 93.99 101.92 P 1 1 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 0.027347 0.005772 0.003204 0.00000 SCALE2 0.000000 0.026478 0.005747 0.00000 SCALE3 0.000000 0.000000 0.017254 0.00000 CONECT 13 2306 CONECT 2306 13 CONECT 2318 2319 2320 2321 CONECT 2319 2318 CONECT 2320 2318 CONECT 2321 2318 2322 2323 CONECT 2322 2321 CONECT 2323 2321 2324 CONECT 2324 2323 2325 2326 CONECT 2325 2324 CONECT 2326 2324 CONECT 2327 2328 2329 2330 CONECT 2328 2327 CONECT 2329 2327 CONECT 2330 2327 2331 2332 CONECT 2331 2330 CONECT 2332 2330 2333 CONECT 2333 2332 2334 2335 CONECT 2334 2333 CONECT 2335 2333 CONECT 2336 2337 2338 CONECT 2337 2336 CONECT 2338 2336 2339 2340 CONECT 2339 2338 CONECT 2340 2338 2341 CONECT 2341 2340 CONECT 2342 2343 2344 CONECT 2343 2342 CONECT 2344 2342 2345 2346 CONECT 2345 2344 CONECT 2346 2344 2347 CONECT 2347 2346 CONECT 2348 2349 2350 CONECT 2349 2348 CONECT 2350 2348 2351 2352 CONECT 2351 2350 CONECT 2352 2350 2353 CONECT 2353 2352 CONECT 2354 2355 2356 2357 2358 CONECT 2355 2354 CONECT 2356 2354 CONECT 2357 2354 CONECT 2358 2354 MASTER 248 0 6 6 0 0 0 6 2386 1 43 26 END