HEADER DE NOVO PROTEIN 27-AUG-24 9DD3 TITLE CRYSTAL STRUCTURE OF DESIGNED ALLOSTERIC FACILITATED DISSOCIATION TITLE 2 SWITCH AS5 IN COMPLEX STATE HE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED ALLOSTERIC FACILITATED DISSOCIATION SWITCH AS5 H; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DESIGNED ALLOSTERIC FACILITATED DISSOCIATION SWITCH AS5 E; COMPND 7 CHAIN: B; COMPND 8 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; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN, DESIGN MODEL, EFFECTOR, KINETICS AND DYNAMICS, KEYWDS 2 PROTEIN-PROTEIN INTERACTIONS EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,A.BROERMAN,D.BAKER REVDAT 4 19-NOV-25 9DD3 1 JRNL REVDAT 3 08-OCT-25 9DD3 1 JRNL REVDAT 2 24-SEP-25 9DD3 1 JRNL REVDAT 1 20-AUG-25 9DD3 0 JRNL AUTH A.J.BROERMAN,C.POLLMANN,Y.ZHAO,M.A.LICHTENSTEIN,M.D.JACKSON, JRNL AUTH 2 M.H.TESSMER,W.H.RYU,M.OGISHI,M.H.ABEDI,D.D.SAHTOE,A.ALLEN, JRNL AUTH 3 A.KANG,J.DE LA CRUZ,E.BRACKENBROUGH,B.SANKARAN,A.K.BERA, JRNL AUTH 4 D.M.ZUCKERMAN,S.STOLL,K.C.GARCIA,F.PRAETORIUS,J.PIEHLER, JRNL AUTH 5 D.BAKER JRNL TITL DESIGN OF FACILITATED DISSOCIATION ENABLES TIMING OF JRNL TITL 2 CYTOKINE SIGNALLING. JRNL REF NATURE V. 647 528 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 40993395 JRNL DOI 10.1038/S41586-025-09549-Z REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 24348 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.620 REMARK 3 FREE R VALUE TEST SET COUNT : 1855 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 31.6900 - 3.8500 0.83 1645 136 0.1801 0.2274 REMARK 3 2 3.8500 - 3.0600 0.86 1663 137 0.1908 0.2109 REMARK 3 3 3.0600 - 2.6700 0.89 1696 140 0.2001 0.2545 REMARK 3 4 2.6700 - 2.4300 0.90 1720 142 0.1992 0.2880 REMARK 3 5 2.4300 - 2.2600 0.89 1692 140 0.1951 0.2325 REMARK 3 6 2.2500 - 2.1200 0.90 1695 139 0.1919 0.2723 REMARK 3 7 2.1200 - 2.0200 0.91 1749 144 0.2059 0.2903 REMARK 3 8 2.0200 - 1.9300 0.93 1759 145 0.2384 0.2956 REMARK 3 9 1.9300 - 1.8500 0.94 1749 144 0.2473 0.3058 REMARK 3 10 1.8500 - 1.7900 0.94 1779 147 0.2548 0.3405 REMARK 3 11 1.7900 - 1.7300 0.95 1780 147 0.2731 0.2938 REMARK 3 12 1.7300 - 1.6800 0.94 1793 148 0.3027 0.3393 REMARK 3 13 1.6800 - 1.6400 0.95 1773 146 0.3238 0.3456 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) : 0.235 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.619 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.23 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 : 0.003 2161 REMARK 3 ANGLE : 0.525 2905 REMARK 3 CHIRALITY : 0.037 355 REMARK 3 PLANARITY : 0.005 374 REMARK 3 DIHEDRAL : 3.810 302 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 9DD3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92009 REMARK 200 MONOCHROMATOR : SI(111) DCM REMARK 200 OPTICS : HORIZONTAL PRE-FOCUS BIMORPH REMARK 200 MIRROR & KB BIMORPH MIRRORS 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 31.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.06200 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 (%): 28.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M TRIS PH 8.5 AND 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 45.08550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.83150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.08550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.83150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 -2 REMARK 465 SER A -1 REMARK 465 GLU B 1 REMARK 465 GLU B 2 REMARK 465 ARG B 3 REMARK 465 LYS B 24 REMARK 465 GLU B 25 REMARK 465 GLU B 26 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 207 CG CD NE CZ NH1 NH2 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 VAL A 201 -166.74 -115.73 REMARK 500 LYS A 247 -146.15 -108.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 9DD3 A -2 257 PDB 9DD3 9DD3 -2 257 DBREF 9DD3 B 1 26 PDB 9DD3 9DD3 1 26 SEQRES 1 A 260 MET SER GLY SER LEU ARG GLU GLU ILE ARG LYS LEU ALA SEQRES 2 A 260 GLU GLN LEU SER GLU LYS TYR LYS ASP GLU GLU ILE ARG SEQRES 3 A 260 GLU LEU ALA ARG GLU ALA ALA GLU LEU ALA GLU GLU SER SEQRES 4 A 260 ASP ASP PRO GLU VAL LEU GLU LEU ALA TYR GLU ALA LEU SEQRES 5 A 260 LYS LYS GLY LEU GLU LEU GLU ASP GLU GLU LYS VAL LYS SEQRES 6 A 260 LEU ILE LEU LEU ALA ALA VAL LEU ALA ALA ARG VAL ALA SEQRES 7 A 260 ARG GLY GLU VAL PRO GLU GLU LYS LEU GLU ILE ALA LEU SEQRES 8 A 260 LYS ALA LEU GLU LEU ALA GLU ALA SER GLU ASP GLU ARG SEQRES 9 A 260 ILE ILE ARG GLY ALA LEU ARG ALA ALA LEU ALA ALA ALA SEQRES 10 A 260 ARG THR ASP ASP PRO LEU ALA LEU GLU VAL VAL LEU GLU SEQRES 11 A 260 ALA LEU GLU ARG ALA GLN ALA SER GLU ASP GLU ARG LEU SEQRES 12 A 260 ILE ARG ALA ILE LEU ALA ALA ALA TYR ALA PHE ALA LEU SEQRES 13 A 260 LEU ALA VAL ALA GLY ALA SER ALA GLU ARG LEU LYS GLU SEQRES 14 A 260 ALA GLU ALA ILE VAL LYS GLU LEU ILE ALA ALA ALA GLU SEQRES 15 A 260 LYS GLY ALA SER PRO GLN GLU LEU VAL LEU LEU VAL ILE SEQRES 16 A 260 GLU MET MET VAL LYS GLY MET GLY VAL THR MET GLU THR SEQRES 17 A 260 HIS ARG SER GLY ASN GLU VAL LYS VAL VAL ILE LYS GLY SEQRES 18 A 260 LEU HIS GLU SER GLN GLN GLU VAL LEU LEU GLU ALA VAL SEQRES 19 A 260 LEU PHE ALA ALA GLU LEU MET GLY VAL ARG VAL ARG ILE SEQRES 20 A 260 ARG PHE LYS GLY ASP THR VAL THR ILE VAL VAL ARG GLU SEQRES 1 B 26 GLU GLU ARG LYS LYS GLU LEU ALA LYS GLU VAL ILE GLU SEQRES 2 B 26 THR ALA LYS LYS LEU ILE GLU LYS LEU ALA LYS GLU GLU FORMUL 3 HOH *70(H2 O) HELIX 1 AA1 GLY A 0 TYR A 17 1 18 HELIX 2 AA2 ASP A 19 SER A 36 1 18 HELIX 3 AA3 ASP A 38 LEU A 55 1 18 HELIX 4 AA4 ASP A 57 ARG A 76 1 20 HELIX 5 AA5 PRO A 80 SER A 97 1 18 HELIX 6 AA6 ASP A 99 THR A 116 1 18 HELIX 7 AA7 ASP A 118 SER A 135 1 18 HELIX 8 AA8 ASP A 137 ALA A 157 1 21 HELIX 9 AA9 SER A 160 LYS A 180 1 21 HELIX 10 AB1 SER A 183 MET A 199 1 17 HELIX 11 AB2 HIS A 220 GLY A 239 1 20 HELIX 12 AB3 LYS B 5 ALA B 23 1 19 SHEET 1 AA1 4 THR A 202 ARG A 207 0 SHEET 2 AA1 4 VAL A 212 LYS A 217 -1 O LYS A 213 N HIS A 206 SHEET 3 AA1 4 THR A 250 VAL A 255 -1 O VAL A 251 N ILE A 216 SHEET 4 AA1 4 VAL A 242 PHE A 246 -1 N ARG A 245 O THR A 252 CRYST1 90.171 35.663 75.522 90.00 116.20 90.00 C 1 2 1 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 0.011090 0.000000 0.005457 0.00000 SCALE2 0.000000 0.028040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014757 0.00000 MASTER 247 0 0 12 4 0 0 6 2202 2 0 22 END