HEADER DE NOVO PROTEIN 08-JUN-25 9RGY TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED SINGLE-CHAIN TITLE 2 ANTIPARALLEL 3-HELIX COILED-COIL BUNDLE, SC-APCC3-CW-0NTT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC3-CW-0NTT; COMPND 3 CHAIN: A, B; 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, CC, DE NOVO, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.LENG,D.N.WOOLFSON REVDAT 3 22-OCT-25 9RGY 1 JRNL REVDAT 2 01-OCT-25 9RGY 1 JRNL REVDAT 1 03-SEP-25 9RGY 0 JRNL AUTH X.LENG,K.I.ALBANESE,L.R.GOLUB,A.A.NORMAN,J.CLAYDEN, JRNL AUTH 2 D.N.WOOLFSON JRNL TITL DE NOVO DESIGNED 3-HELIX BUNDLE PEPTIDES AND PROTEINS WITH JRNL TITL 2 CONTROLLED TOPOLOGY AND STABILITY. JRNL REF CHEM SCI V. 16 18632 2025 JRNL REFN ISSN 2041-6520 JRNL PMID 40969159 JRNL DOI 10.1039/D5SC05576H REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18502 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 923 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 32.2200 - 3.6300 1.00 2590 143 0.1789 0.1818 REMARK 3 2 3.6300 - 2.8800 1.00 2536 124 0.1720 0.1931 REMARK 3 3 2.8800 - 2.5200 1.00 2484 146 0.1866 0.2391 REMARK 3 4 2.5200 - 2.2900 1.00 2502 124 0.1749 0.2111 REMARK 3 5 2.2900 - 2.1300 1.00 2511 119 0.1750 0.2059 REMARK 3 6 2.1300 - 2.0000 1.00 2476 139 0.1873 0.2682 REMARK 3 7 2.0000 - 1.9000 1.00 2480 128 0.2258 0.2737 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) : 0.198 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.48 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 : 0.008 1432 REMARK 3 ANGLE : 0.765 1937 REMARK 3 CHIRALITY : 0.035 244 REMARK 3 PLANARITY : 0.005 238 REMARK 3 DIHEDRAL : 16.267 537 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 19 THROUGH 116) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8918 -0.7200 13.0910 REMARK 3 T TENSOR REMARK 3 T11: 0.1681 T22: 0.1267 REMARK 3 T33: 0.1275 T12: -0.0023 REMARK 3 T13: -0.0042 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.7339 L22: 1.5775 REMARK 3 L33: 1.8350 L12: 0.2360 REMARK 3 L13: -0.4539 L23: -0.5509 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: -0.0369 S13: -0.0073 REMARK 3 S21: 0.1994 S22: 0.0323 S23: 0.0510 REMARK 3 S31: 0.1366 S32: -0.1411 S33: -0.0230 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 22 THROUGH 116) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3091 13.6210 9.7471 REMARK 3 T TENSOR REMARK 3 T11: 0.1806 T22: 0.2567 REMARK 3 T33: 0.2646 T12: 0.0412 REMARK 3 T13: 0.0291 T23: 0.0281 REMARK 3 L TENSOR REMARK 3 L11: 0.6225 L22: 1.5172 REMARK 3 L33: 1.2500 L12: -0.0630 REMARK 3 L13: 0.1191 L23: -0.6001 REMARK 3 S TENSOR REMARK 3 S11: -0.0881 S12: -0.0927 S13: 0.0190 REMARK 3 S21: 0.2354 S22: 0.2189 S23: 0.3398 REMARK 3 S31: -0.0482 S32: -0.3528 S33: -0.1085 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 9RGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1292148399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.6199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18511 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 32.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.10070 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35150 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.610 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 (%): 47.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE 0.1 M MES 30 % REMARK 280 W/V PEG 5000 MME, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 53.70450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.70450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.56000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 HIS B 8 REMARK 465 HIS B 9 REMARK 465 HIS B 10 REMARK 465 SER B 11 REMARK 465 SER B 12 REMARK 465 GLY B 13 REMARK 465 LEU B 14 REMARK 465 VAL B 15 REMARK 465 PRO B 16 REMARK 465 ARG B 17 REMARK 465 GLY B 18 REMARK 465 SER B 19 REMARK 465 HIS B 20 REMARK 465 MET B 21 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 GLU A 35 CG CD OE1 OE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 LYS A 105 CE NZ REMARK 470 GLU B 28 CG CD OE1 OE2 REMARK 470 LYS B 43 CE NZ REMARK 470 LYS B 69 CD CE NZ REMARK 470 LEU B 81 CG CD1 CD2 REMARK 470 ASN B 86 CG OD1 ND2 REMARK 470 LYS B 91 CG CD CE NZ REMARK 470 GLU B 96 CG CD OE1 OE2 REMARK 470 LYS B 97 CG CD CE NZ REMARK 470 LYS B 98 CE NZ 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 ASN B 86 72.21 -118.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 9RGY A 1 116 PDB 9RGY 9RGY 1 116 DBREF 9RGY B 1 116 PDB 9RGY 9RGY 1 116 SEQRES 1 A 116 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 116 LEU VAL PRO ARG GLY SER HIS MET MET LEU ALA ALA LEU SEQRES 3 A 116 LYS GLU LYS LEU ALA ALA LEU LYS GLU LYS LEU ALA ALA SEQRES 4 A 116 LEU LYS TYR LYS LEU ALA ALA LEU LYS GLU LYS LEU GLY SEQRES 5 A 116 LEU THR PRO GLU LEU ALA ALA LEU GLU LYS GLU LEU ALA SEQRES 6 A 116 ALA LEU GLU LYS GLU LEU ALA ALA LEU GLU TRP GLU LEU SEQRES 7 A 116 ALA ALA LEU GLU ALA ASP PRO ASN PRO ASP PRO ALA LYS SEQRES 8 A 116 LEU ALA ALA LEU GLU LYS LYS LEU ALA ALA LEU GLU LYS SEQRES 9 A 116 LYS LEU ALA ALA LEU GLU TYR LYS LEU ALA ALA LEU SEQRES 1 B 116 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 116 LEU VAL PRO ARG GLY SER HIS MET MET LEU ALA ALA LEU SEQRES 3 B 116 LYS GLU LYS LEU ALA ALA LEU LYS GLU LYS LEU ALA ALA SEQRES 4 B 116 LEU LYS TYR LYS LEU ALA ALA LEU LYS GLU LYS LEU GLY SEQRES 5 B 116 LEU THR PRO GLU LEU ALA ALA LEU GLU LYS GLU LEU ALA SEQRES 6 B 116 ALA LEU GLU LYS GLU LEU ALA ALA LEU GLU TRP GLU LEU SEQRES 7 B 116 ALA ALA LEU GLU ALA ASP PRO ASN PRO ASP PRO ALA LYS SEQRES 8 B 116 LEU ALA ALA LEU GLU LYS LYS LEU ALA ALA LEU GLU LYS SEQRES 9 B 116 LYS LEU ALA ALA LEU GLU TYR LYS LEU ALA ALA LEU FORMUL 3 HOH *361(H2 O) HELIX 1 AA1 SER A 19 GLY A 52 1 34 HELIX 2 AA2 THR A 54 ASP A 84 1 31 HELIX 3 AA3 ASP A 88 ALA A 115 1 28 HELIX 4 AA4 LEU B 23 GLY B 52 1 30 HELIX 5 AA5 THR B 54 ASP B 84 1 31 HELIX 6 AA6 ASP B 88 ALA B 115 1 28 CRYST1 107.409 37.120 63.433 90.00 112.62 90.00 C 1 2 1 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 0.009310 0.000000 0.003879 0.00000 SCALE2 0.000000 0.026940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017078 0.00000 MASTER 314 0 0 6 0 0 0 6 1778 2 0 18 END