HEADER DE NOVO PROTEIN 27-AUG-24 9DD4 TITLE CRYSTAL STRUCTURE OF DESIGNED FACILITATED DISSOCIATION TARGET TITLE 2 LHD101AN1: LHD101A WITH AN N-TERMINAL EXTENSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED FACILITATED DISSOCIATION TARGET LHD101AN1: LHD101A COMPND 3 WITH AN N-TERMINAL EXTENSION; COMPND 4 CHAIN: A, B; COMPND 5 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 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 9DD4 1 JRNL REVDAT 3 08-OCT-25 9DD4 1 JRNL REVDAT 2 24-SEP-25 9DD4 1 JRNL REVDAT 1 20-AUG-25 9DD4 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. 2.11 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 20779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1716 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 51.8800 - 4.8300 0.99 1698 157 0.1893 0.2506 REMARK 3 2 4.8300 - 3.8300 1.00 1611 150 0.1899 0.2128 REMARK 3 3 3.8300 - 3.3500 0.99 1586 142 0.2171 0.2637 REMARK 3 4 3.3500 - 3.0400 1.00 1597 139 0.2633 0.3182 REMARK 3 5 3.0400 - 2.8200 1.00 1567 148 0.2863 0.2910 REMARK 3 6 2.8200 - 2.6600 1.00 1595 140 0.2607 0.3054 REMARK 3 7 2.6600 - 2.5300 1.00 1564 143 0.2849 0.2916 REMARK 3 8 2.5300 - 2.4200 1.00 1582 135 0.2913 0.3376 REMARK 3 9 2.4200 - 2.3200 1.00 1539 152 0.2850 0.2838 REMARK 3 10 2.3200 - 2.2400 1.00 1575 135 0.2688 0.3203 REMARK 3 11 2.2400 - 2.1700 1.00 1560 152 0.2619 0.3320 REMARK 3 12 2.1700 - 2.1100 1.00 1589 123 0.3093 0.3054 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) : 0.261 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.949 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.57 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 : 0.002 1992 REMARK 3 ANGLE : 0.339 2674 REMARK 3 CHIRALITY : 0.039 310 REMARK 3 PLANARITY : 0.003 354 REMARK 3 DIHEDRAL : 11.474 780 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 2:124 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.761 17.091 -15.487 REMARK 3 T TENSOR REMARK 3 T11: 0.2578 T22: 0.4294 REMARK 3 T33: 0.3956 T12: 0.0395 REMARK 3 T13: 0.0128 T23: -0.0321 REMARK 3 L TENSOR REMARK 3 L11: 6.5850 L22: 8.3101 REMARK 3 L33: 9.8009 L12: -2.9094 REMARK 3 L13: 3.0672 L23: -1.5453 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: -0.1219 S13: 0.0837 REMARK 3 S21: -0.0549 S22: 0.1006 S23: 0.2062 REMARK 3 S31: 0.0131 S32: 0.0972 S33: -0.1576 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND RESID 2:124 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.550 2.645 -0.168 REMARK 3 T TENSOR REMARK 3 T11: 0.3774 T22: 0.5143 REMARK 3 T33: 0.4609 T12: 0.0172 REMARK 3 T13: -0.0893 T23: -0.0499 REMARK 3 L TENSOR REMARK 3 L11: 4.8679 L22: 9.4303 REMARK 3 L33: 6.7265 L12: 1.7235 REMARK 3 L13: 2.1348 L23: 0.2364 REMARK 3 S TENSOR REMARK 3 S11: 0.0816 S12: -0.0242 S13: -0.0895 REMARK 3 S21: 0.1934 S22: -0.1562 S23: -0.2481 REMARK 3 S31: 0.0193 S32: -0.1514 S33: 0.1014 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 9DD4 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_1000287670. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20779 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 51.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.91100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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 (%): 58.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.0, 5% W/V REMARK 280 GAMMA-PGA (NA+ FROM, LM) AND 30% V/V PEG 400, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 32.48600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.19650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.33300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.19650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.48600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.33300 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 -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 GLU A 1 REMARK 465 GLY A 125 REMARK 465 SER A 126 REMARK 465 GLY A 127 REMARK 465 MET B -2 REMARK 465 SER B -1 REMARK 465 GLY B 0 REMARK 465 GLU B 1 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 GLY B 127 DBREF 9DD4 A -2 127 PDB 9DD4 9DD4 -2 127 DBREF 9DD4 B -2 127 PDB 9DD4 9DD4 -2 127 SEQRES 1 A 130 MET SER GLY GLU GLU ALA VAL ARG ARG ARG PHE GLU GLU SEQRES 2 A 130 LEU LEU ARG GLU ALA LEU ALA PHE ARG GLU ARG THR GLY SEQRES 3 A 130 GLY ARG ARG GLU THR LEU GLU HIS ALA VAL ARG LEU ALA SEQRES 4 A 130 ARG GLU LEU ALA GLU PHE ALA ALA SER HIS PRO GLU PHE SEQRES 5 A 130 ASN ARG GLN GLU ALA VAL LEU LEU ALA ILE GLU LEU MET SEQRES 6 A 130 VAL ARG ALA MET GLY VAL THR MET GLU THR HIS ARG SER SEQRES 7 A 130 GLY ASN GLU VAL LYS VAL VAL ILE LYS GLY LEU ASN ILE SEQRES 8 A 130 ASP GLU GLN ARG ALA LEU TYR ARG ALA VAL ARG GLU THR SEQRES 9 A 130 SER LYS ILE MET GLY VAL GLU THR GLU ILE GLU VAL GLU SEQRES 10 A 130 GLY ASP THR VAL THR ILE VAL VAL ARG GLU GLY SER GLY SEQRES 1 B 130 MET SER GLY GLU GLU ALA VAL ARG ARG ARG PHE GLU GLU SEQRES 2 B 130 LEU LEU ARG GLU ALA LEU ALA PHE ARG GLU ARG THR GLY SEQRES 3 B 130 GLY ARG ARG GLU THR LEU GLU HIS ALA VAL ARG LEU ALA SEQRES 4 B 130 ARG GLU LEU ALA GLU PHE ALA ALA SER HIS PRO GLU PHE SEQRES 5 B 130 ASN ARG GLN GLU ALA VAL LEU LEU ALA ILE GLU LEU MET SEQRES 6 B 130 VAL ARG ALA MET GLY VAL THR MET GLU THR HIS ARG SER SEQRES 7 B 130 GLY ASN GLU VAL LYS VAL VAL ILE LYS GLY LEU ASN ILE SEQRES 8 B 130 ASP GLU GLN ARG ALA LEU TYR ARG ALA VAL ARG GLU THR SEQRES 9 B 130 SER LYS ILE MET GLY VAL GLU THR GLU ILE GLU VAL GLU SEQRES 10 B 130 GLY ASP THR VAL THR ILE VAL VAL ARG GLU GLY SER GLY FORMUL 3 HOH *16(H2 O) HELIX 1 AA1 GLU A 2 THR A 22 1 21 HELIX 2 AA2 GLY A 24 SER A 45 1 22 HELIX 3 AA3 ASN A 50 GLY A 67 1 18 HELIX 4 AA4 ASN A 87 GLY A 106 1 20 HELIX 5 AA5 ALA B 3 THR B 22 1 20 HELIX 6 AA6 GLY B 24 SER B 45 1 22 HELIX 7 AA7 ASN B 50 GLY B 67 1 18 HELIX 8 AA8 ASN B 87 GLY B 106 1 20 SHEET 1 AA1 4 THR A 69 SER A 75 0 SHEET 2 AA1 4 GLU A 78 LYS A 84 -1 O GLU A 78 N SER A 75 SHEET 3 AA1 4 THR A 117 VAL A 122 -1 O ILE A 120 N VAL A 81 SHEET 4 AA1 4 THR A 109 GLU A 114 -1 N GLU A 112 O THR A 119 SHEET 1 AA2 4 THR B 69 SER B 75 0 SHEET 2 AA2 4 GLU B 78 LYS B 84 -1 O LYS B 80 N HIS B 73 SHEET 3 AA2 4 THR B 117 ARG B 123 -1 O ILE B 120 N VAL B 81 SHEET 4 AA2 4 GLU B 108 GLU B 114 -1 N GLU B 112 O THR B 119 CRYST1 64.972 70.666 76.393 90.00 90.00 90.00 P 21 21 21 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 0.015391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013090 0.00000 MASTER 257 0 0 8 8 0 0 6 1990 2 0 20 END