HEADER APOPTOSIS 17-JUN-26 36LX TITLE CRYSTAL STRUCTURE OF MINI-BINDER MB03-DS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MB03-DS; COMPND 3 CHAIN: A, B, C, D; 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 DE NOVO DESIGN, DEEP LEARNING, MINIBINDER, BACTEROIDES FRAGILIS KEYWDS 2 TOXIN, RECEPTOR, PATHOLOGY, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,V.ADEBOMI,P.SRINIVAS,A.KANG,G.BHARDWAJ REVDAT 1 15-JUL-26 36LX 0 JRNL AUTH P.SRINIVAS,V.ADEBOMI,S.M.MARKIEWICZ,K.WANG,D.CHAC, JRNL AUTH 2 K.LINDENAUER,N.HUBER,Z.TAO,P.LUONG,S.A.RETTIE,M.W.SMITH, JRNL AUTH 3 A.K.BERA,A.KANG,H.NGUYEN,M.SCHNEIDER,Y.WANG,S.B.PETERSON, JRNL AUTH 4 M.DONG,A.A.WEIL,G.BHARDWAJ,J.D.MOUGOUS JRNL TITL ORALLY AVAILABLE DESIGNED MINIPROTEINS INHIBIT JRNL TITL 2 ENTEROTOXIGENIC BACTEROIDES FRAGILIS PATHOLOGY BY BLOCKING JRNL TITL 3 TOXIN RECEPTOR BINDING. JRNL REF BIORXIV 2026 JRNL REFN ISSN 2692-8205 JRNL PMID 42395444 JRNL DOI 10.64898/2026.06.22.733822 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 14077 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1408 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 40.0000 - 4.5200 0.99 1389 154 0.2464 0.2543 REMARK 3 2 4.5200 - 3.5900 0.98 1303 146 0.2226 0.2624 REMARK 3 3 3.5900 - 3.1400 0.98 1290 144 0.2491 0.2807 REMARK 3 4 3.1400 - 2.8500 0.99 1295 144 0.2735 0.3492 REMARK 3 5 2.8500 - 2.6500 0.99 1283 142 0.2634 0.3075 REMARK 3 6 2.6500 - 2.4900 0.99 1257 140 0.2675 0.3244 REMARK 3 7 2.4900 - 2.3700 0.98 1263 140 0.2648 0.2907 REMARK 3 8 2.3700 - 2.2600 0.97 1246 137 0.2722 0.2987 REMARK 3 9 2.2600 - 2.1800 0.94 1197 134 0.2806 0.3170 REMARK 3 10 2.1800 - 2.1000 0.90 1146 127 0.3122 0.3560 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) : 0.287 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.91 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 1898 REMARK 3 ANGLE : 0.476 2535 REMARK 3 CHIRALITY : 0.031 288 REMARK 3 PLANARITY : 0.002 318 REMARK 3 DIHEDRAL : 20.605 765 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 36LX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-26. REMARK 100 THE DEPOSITION ID IS D_1000309113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91992 REMARK 200 MONOCHROMATOR : HORIZONTAL DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR (DCM) REMARK 200 OPTICS : HORIZONTAL SECONDARY SOURCE 2 REMARK 200 STAGE FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14230 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.94500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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 (%): 36.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24 %(W/V) PEG 1500 AND 20% (W/V) REMARK 280 GLYCEROL, VAPOR DIFFUSION, 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 22.13250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.71600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.70600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.71600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.13250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.70600 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, 3, 4 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 SER A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 GLU A 58 REMARK 465 ASN A 59 REMARK 465 LEU A 60 REMARK 465 TYR A 61 REMARK 465 PHE A 62 REMARK 465 GLN A 63 REMARK 465 GLY A 64 REMARK 465 GLU B 58 REMARK 465 ASN B 59 REMARK 465 LEU B 60 REMARK 465 TYR B 61 REMARK 465 PHE B 62 REMARK 465 GLN B 63 REMARK 465 GLY B 64 REMARK 465 GLU C 58 REMARK 465 ASN C 59 REMARK 465 LEU C 60 REMARK 465 TYR C 61 REMARK 465 PHE C 62 REMARK 465 GLN C 63 REMARK 465 GLY C 64 REMARK 465 SER D -2 REMARK 465 GLY D -1 REMARK 465 GLY D 0 REMARK 465 GLU D 58 REMARK 465 ASN D 59 REMARK 465 LEU D 60 REMARK 465 TYR D 61 REMARK 465 PHE D 62 REMARK 465 GLN D 63 REMARK 465 GLY D 64 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 LYS C 18 -50.73 -128.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 36LX A -2 64 PDB 36LX 36LX -2 64 DBREF 36LX B -2 64 PDB 36LX 36LX -2 64 DBREF 36LX C -2 64 PDB 36LX 36LX -2 64 DBREF 36LX D -2 64 PDB 36LX 36LX -2 64 SEQRES 1 A 67 SER GLY GLY SER GLU GLU CYS LYS LYS LYS ILE GLU GLU SEQRES 2 A 67 MET LEU GLU GLU ALA LYS LYS LYS ASP PRO ALA LEU TYR SEQRES 3 A 67 GLU TYR LEU THR LYS SER LEU ASP ILE LEU GLU LYS MET SEQRES 4 A 67 GLY ALA SER CYS GLU ASP LYS LEU PHE ASN LEU GLU VAL SEQRES 5 A 67 VAL SER GLN VAL TYR LEU ASN THR GLU ASN LEU TYR PHE SEQRES 6 A 67 GLN GLY SEQRES 1 B 67 SER GLY GLY SER GLU GLU CYS LYS LYS LYS ILE GLU GLU SEQRES 2 B 67 MET LEU GLU GLU ALA LYS LYS LYS ASP PRO ALA LEU TYR SEQRES 3 B 67 GLU TYR LEU THR LYS SER LEU ASP ILE LEU GLU LYS MET SEQRES 4 B 67 GLY ALA SER CYS GLU ASP LYS LEU PHE ASN LEU GLU VAL SEQRES 5 B 67 VAL SER GLN VAL TYR LEU ASN THR GLU ASN LEU TYR PHE SEQRES 6 B 67 GLN GLY SEQRES 1 C 67 SER GLY GLY SER GLU GLU CYS LYS LYS LYS ILE GLU GLU SEQRES 2 C 67 MET LEU GLU GLU ALA LYS LYS LYS ASP PRO ALA LEU TYR SEQRES 3 C 67 GLU TYR LEU THR LYS SER LEU ASP ILE LEU GLU LYS MET SEQRES 4 C 67 GLY ALA SER CYS GLU ASP LYS LEU PHE ASN LEU GLU VAL SEQRES 5 C 67 VAL SER GLN VAL TYR LEU ASN THR GLU ASN LEU TYR PHE SEQRES 6 C 67 GLN GLY SEQRES 1 D 67 SER GLY GLY SER GLU GLU CYS LYS LYS LYS ILE GLU GLU SEQRES 2 D 67 MET LEU GLU GLU ALA LYS LYS LYS ASP PRO ALA LEU TYR SEQRES 3 D 67 GLU TYR LEU THR LYS SER LEU ASP ILE LEU GLU LYS MET SEQRES 4 D 67 GLY ALA SER CYS GLU ASP LYS LEU PHE ASN LEU GLU VAL SEQRES 5 D 67 VAL SER GLN VAL TYR LEU ASN THR GLU ASN LEU TYR PHE SEQRES 6 D 67 GLN GLY FORMUL 5 HOH *43(H2 O) HELIX 1 AA1 GLU A 2 ASP A 19 1 18 HELIX 2 AA2 ASP A 19 GLY A 37 1 19 HELIX 3 AA3 SER A 39 ASN A 56 1 18 HELIX 4 AA4 GLY B -1 ASP B 19 1 21 HELIX 5 AA5 ASP B 19 GLY B 37 1 19 HELIX 6 AA6 SER B 39 THR B 57 1 19 HELIX 7 AA7 GLY C -1 ASP C 19 1 21 HELIX 8 AA8 ASP C 19 GLY C 37 1 19 HELIX 9 AA9 SER C 39 THR C 57 1 19 HELIX 10 AB1 GLU D 2 ASP D 19 1 18 HELIX 11 AB2 ASP D 19 GLY D 37 1 19 HELIX 12 AB3 SER D 39 THR D 57 1 19 SSBOND 1 CYS A 4 CYS A 40 1555 1555 2.03 SSBOND 2 CYS B 4 CYS B 40 1555 1555 2.04 SSBOND 3 CYS C 4 CYS C 40 1555 1555 2.04 SSBOND 4 CYS D 4 CYS D 40 1555 1555 2.03 CRYST1 44.265 57.412 93.432 90.00 90.00 90.00 P 21 21 21 16 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 0.022591 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010703 0.00000 CONECT 24 313 CONECT 313 24 CONECT 499 794 CONECT 794 499 CONECT 980 1269 CONECT 1269 980 CONECT 1441 1741 CONECT 1741 1441 MASTER 279 0 0 12 0 0 0 6 1905 4 8 24 END