HEADER DE NOVO PROTEIN 11-DEC-25 9TLL TITLE DE NOVO DESIGNED SINGLE-CHAIN ANTIPARALLEL COILED-COIL HAIRPIN, SC- TITLE 2 APCC-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC-2; 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 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PROTEIN BINDER, COMPUTATIONAL DESIGN, COILED-COIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.MYLEMANS,D.N.WOOLFSON REVDAT 1 19-AUG-26 9TLL 0 JRNL AUTH B.MYLEMANS,B.KORONA,A.M.ACEVEDO-JAKE,A.MACRAE,T.A.EDWARDS, JRNL AUTH 2 D.T.HUANG,A.J.WILSON,L.S.ITZHAKI,D.N.WOOLFSON JRNL TITL DE NOVO-DESIGNED BIFUNCTIONAL JRNL REF J.AM.CHEM.SOC. 2026 JRNL REFN ESSN 1520-5126 JRNL DOI 10.1021/JACS.6C07593 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 12808 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 : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 617 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 34.1100 - 2.3800 0.99 3073 166 0.1822 0.1883 REMARK 3 2 2.3800 - 1.8900 1.00 3067 131 0.1932 0.2008 REMARK 3 3 1.8900 - 1.6500 1.00 3036 184 0.1540 0.1956 REMARK 3 4 1.6500 - 1.5000 0.99 3015 136 0.1798 0.2263 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) : 0.115 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.797 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.44 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 : 0.009 580 REMARK 3 ANGLE : 1.067 780 REMARK 3 CHIRALITY : 0.039 82 REMARK 3 PLANARITY : 0.007 100 REMARK 3 DIHEDRAL : 15.604 227 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): 15.9912 -0.7252 5.7183 REMARK 3 T TENSOR REMARK 3 T11: 0.0653 T22: 0.0871 REMARK 3 T33: 0.0758 T12: 0.0238 REMARK 3 T13: 0.0207 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 1.0720 L22: 1.5864 REMARK 3 L33: 1.3946 L12: 0.6471 REMARK 3 L13: -0.0510 L23: -0.1929 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.0547 S13: 0.1253 REMARK 3 S21: 0.1458 S22: 0.0332 S23: 0.2453 REMARK 3 S31: -0.0031 S32: -0.0935 S33: -0.0542 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 9TLL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1292152370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 34.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M REMARK 280 PHOSPHATE/CITRATE, 20% W/V PEG 1000, PH 4.2, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 24.11850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 24.11850 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.13600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.11850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.56800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.11850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.70400 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.11850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.11850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.13600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 24.11850 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.70400 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 24.11850 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 17.56800 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 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 6 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 9 CD NE CZ NH1 NH2 REMARK 470 ARG A 37 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 68 CA - C - N ANGL. DEV. = -20.7 DEGREES REMARK 500 GLY A 68 O - C - N ANGL. DEV. = 12.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 35 65.61 -150.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 107 DBREF 9TLL A 1 69 PDB 9TLL 9TLL 1 69 SEQRES 1 A 69 ACE ARG ASP ARG SER ARG LEU ALA ARG ARG ARG ALA ALA SEQRES 2 A 69 LEU LYS GLN ARG ILE ALA ALA LEU LYS GLN ARG ARG ALA SEQRES 3 A 69 ALA LEU LYS TRP GLN ILE GLN SER ASP PRO ARG LYS LYS SEQRES 4 A 69 GLN LEU GLU GLN GLU LEU ALA ALA LEU ASP GLN GLU ILE SEQRES 5 A 69 ALA ALA ALA GLU GLN GLU LEU ALA ALA LEU ASP TRP GLN SEQRES 6 A 69 ILE ALA GLY NH2 HET ACE A 1 3 HET NH2 A 69 1 HET SO4 A 101 5 HET SO4 A 102 5 HET GOL A 103 6 HET GOL A 104 6 HET SO4 A 105 5 HET SO4 A 106 5 HET PEG A 107 6 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 SO4 4(O4 S 2-) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 8 PEG C4 H10 O3 FORMUL 9 HOH *48(H2 O) HELIX 1 AA1 ARG A 2 ASP A 35 1 34 HELIX 2 AA2 LYS A 38 GLY A 68 1 31 LINK C ACE A 1 N ARG A 2 1555 1555 1.33 LINK C GLY A 68 N NH2 A 69 1555 1555 1.43 CRYST1 48.237 48.237 70.272 90.00 90.00 90.00 I 41 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 0.020731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020731 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014230 0.00000 CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 541 543 CONECT 543 541 CONECT 545 546 547 548 549 CONECT 546 545 CONECT 547 545 CONECT 548 545 CONECT 549 545 CONECT 550 551 552 553 554 CONECT 551 550 CONECT 552 550 CONECT 553 550 CONECT 554 550 CONECT 555 556 557 CONECT 556 555 CONECT 557 555 558 559 CONECT 558 557 CONECT 559 557 560 CONECT 560 559 CONECT 561 562 563 CONECT 562 561 CONECT 563 561 564 565 CONECT 564 563 CONECT 565 563 566 CONECT 566 565 CONECT 567 568 569 570 571 CONECT 568 567 CONECT 569 567 CONECT 570 567 CONECT 571 567 CONECT 572 573 574 575 576 CONECT 573 572 CONECT 574 572 CONECT 575 572 CONECT 576 572 CONECT 577 578 579 CONECT 578 577 CONECT 579 577 580 CONECT 580 579 581 CONECT 581 580 582 CONECT 582 581 MASTER 277 0 9 2 0 0 0 6 610 1 44 6 END