HEADER DE NOVO PROTEIN 22-AUG-23 8QAF TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED SINGLE-CHAIN TITLE 2 ANTIPARALLEL 8-HELIX COILED-COIL ALPHA-HELICAL BARREL, SC-APCC-8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC-8; 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 COILED COIL, 8-HELIX ANTI-PARALLEL ALPHA-HELICAL BARREL, DE NOVO KEYWDS 2 PROTEIN DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.I.ALBANESE,R.PETRENAS,D.N.WOOLFSON REVDAT 2 07-AUG-24 8QAF 1 JRNL REVDAT 1 03-JUL-24 8QAF 0 JRNL AUTH K.I.ALBANESE,R.PETRENAS,F.PIRRO,E.A.NAUDIN,U.BORUCU, JRNL AUTH 2 W.M.DAWSON,D.A.SCOTT,G.J.LEGGETT,O.D.WEINER,T.A.A.OLIVER, JRNL AUTH 3 D.N.WOOLFSON JRNL TITL RATIONALLY SEEDED COMPUTATIONAL PROTEIN DESIGN OF JRNL TITL 2 ɑ-HELICAL BARRELS. JRNL REF NAT.CHEM.BIOL. V. 20 991 2024 JRNL REFN ESSN 1552-4469 JRNL PMID 38902458 JRNL DOI 10.1038/S41589-024-01642-0 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 5271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 248 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 37.6600 - 2.5200 0.99 2580 126 0.2589 0.2322 REMARK 3 2 2.5200 - 2.0000 1.00 2443 122 0.2113 0.3434 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.629 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.25 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 : 0.006 375 REMARK 3 ANGLE : 0.573 515 REMARK 3 CHIRALITY : 0.044 73 REMARK 3 PLANARITY : 0.004 60 REMARK 3 DIHEDRAL : 3.279 59 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 0 THROUGH 64) REMARK 3 ORIGIN FOR THE GROUP (A): 44.0711 16.6108 12.7104 REMARK 3 T TENSOR REMARK 3 T11: 0.2035 T22: 0.1973 REMARK 3 T33: 0.4914 T12: -0.0420 REMARK 3 T13: -0.0085 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 3.5866 L22: 3.9321 REMARK 3 L33: 6.2262 L12: -0.6004 REMARK 3 L13: -1.1778 L23: 1.1455 REMARK 3 S TENSOR REMARK 3 S11: -0.0207 S12: -0.0665 S13: -0.4944 REMARK 3 S21: 0.0041 S22: -0.0972 S23: 0.3620 REMARK 3 S31: -0.0042 S32: -0.1841 S33: 0.1640 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 8QAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-23 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999 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 : AUTOPROCESS REMARK 200 DATA SCALING SOFTWARE : AUTOPROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5290 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 37.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01179 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.09224 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.240 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 0.1 M BIS TRIS REMARK 280 PROPANE, PH 8.5, 20 % W/V PEG 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.00100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.00100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.00100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.00100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.00100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.00100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.00100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.00100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 100.00400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 50.00200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 75.00300 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 -25.00100 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 25.00100 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 75.00300 REMARK 350 BIOMT3 4 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 -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 VAL A 31 REMARK 465 LYS A 32 REMARK 465 ASP A 33 REMARK 465 PRO A 34 REMARK 465 GLU A 35 REMARK 465 LEU A 36 REMARK 465 ALA A 65 REMARK 465 LYS A 66 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 CB CG SD CE REMARK 470 MET A 1 CB CG SD CE REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 GLU A 5 CD OE1 OE2 REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 GLU A 12 CD OE1 OE2 REMARK 470 LYS A 15 CG CD CE NZ REMARK 470 LYS A 18 CG CD CE NZ REMARK 470 LYS A 19 CE NZ REMARK 470 LYS A 25 CE NZ REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 GLN A 29 CG CD OE1 NE2 REMARK 470 GLN A 30 CB CG CD OE1 NE2 REMARK 470 LYS A 37 CB CG CD CE NZ REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 GLN A 45 CG CD OE1 NE2 REMARK 470 GLU A 48 CD OE1 OE2 REMARK 470 GLU A 49 CG CD OE1 OE2 REMARK 470 LYS A 52 CD CE NZ REMARK 470 LYS A 55 CD CE NZ REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 LYS A 62 CD CE NZ REMARK 470 LYS A 63 CG CD CE NZ DBREF 8QAF A -20 66 PDB 8QAF 8QAF -20 66 SEQRES 1 A 87 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 87 LEU VAL PRO ARG GLY SER HIS MET MET ALA ILE GLU GLU SEQRES 3 A 87 ILE ALA GLN ALA ILE GLU GLU ILE ALA LYS ALA ILE LYS SEQRES 4 A 87 LYS ILE ALA TRP ALA ILE LYS LYS ILE ALA GLN GLN VAL SEQRES 5 A 87 LYS ASP PRO GLU LEU LYS ALA ALA ILE GLU GLU ILE ALA SEQRES 6 A 87 GLN ALA ILE GLU GLU ILE ALA LYS ALA ILE LYS LYS ILE SEQRES 7 A 87 ALA TRP ALA ILE LYS LYS ILE ALA LYS FORMUL 2 HOH *14(H2 O) HELIX 1 AA1 MET A 0 GLN A 30 1 31 HELIX 2 AA2 ALA A 38 ILE A 64 1 27 CRYST1 50.002 50.002 57.249 90.00 90.00 90.00 P 4 21 2 8 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 0.019999 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017468 0.00000