HEADER APOPTOSIS 17-JUN-26 36MB TITLE CRYSTAL STRUCTURE OF MINI-BINDER MB07-DS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MB07-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 36MB 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 21207 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.480 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 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 56.0000 - 4.8200 0.99 1431 144 0.2306 0.2190 REMARK 3 2 4.8200 - 3.8300 1.00 1395 151 0.1817 0.2273 REMARK 3 3 3.8300 - 3.3400 0.99 1370 140 0.2007 0.2387 REMARK 3 4 3.3400 - 3.0400 0.99 1363 145 0.2406 0.2973 REMARK 3 5 3.0400 - 2.8200 0.99 1375 144 0.2425 0.3131 REMARK 3 6 2.8200 - 2.6500 1.00 1384 143 0.2319 0.2858 REMARK 3 7 2.6500 - 2.5200 1.00 1364 140 0.2512 0.2720 REMARK 3 8 2.5200 - 2.4100 1.00 1380 147 0.2439 0.3076 REMARK 3 9 2.4100 - 2.3200 0.98 1354 141 0.2380 0.3037 REMARK 3 10 2.3200 - 2.2400 0.98 1336 145 0.2549 0.3193 REMARK 3 11 2.2400 - 2.1700 0.99 1366 144 0.2531 0.3419 REMARK 3 12 2.1700 - 2.1100 0.99 1372 141 0.2629 0.2912 REMARK 3 13 2.1100 - 2.0500 0.99 1340 130 0.2702 0.3139 REMARK 3 14 2.0500 - 2.0000 0.99 1367 155 0.2919 0.3477 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) : 0.242 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.932 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.06 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 2629 REMARK 3 ANGLE : 0.538 3516 REMARK 3 CHIRALITY : 0.037 403 REMARK 3 PLANARITY : 0.004 445 REMARK 3 DIHEDRAL : 23.013 1105 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 12.2902 -13.8152 15.7628 REMARK 3 T TENSOR REMARK 3 T11: 0.2579 T22: 0.2328 REMARK 3 T33: 0.2469 T12: 0.0086 REMARK 3 T13: -0.0568 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.2752 L22: 0.3034 REMARK 3 L33: 0.2629 L12: 0.0378 REMARK 3 L13: -0.2474 L23: -0.0425 REMARK 3 S TENSOR REMARK 3 S11: -0.0051 S12: -0.0612 S13: -0.0075 REMARK 3 S21: 0.0413 S22: 0.0209 S23: -0.0665 REMARK 3 S31: -0.0160 S32: 0.0899 S33: -0.0177 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 36MB 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_1000309118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97905 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 : 26405 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 56.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.24000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 1.36100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.910 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 (%): 40.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 3.5, 2.0 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.65300 REMARK 290 SMTRY3 2 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 GLY A 80 REMARK 465 SER B -2 REMARK 465 GLY B -1 REMARK 465 GLY B 0 REMARK 465 GLN B 79 REMARK 465 GLY B 80 REMARK 465 SER C -2 REMARK 465 GLY C -1 REMARK 465 GLY C 0 REMARK 465 TYR C 77 REMARK 465 PHE C 78 REMARK 465 GLN C 79 REMARK 465 GLY C 80 REMARK 465 SER D -2 REMARK 465 GLY D -1 REMARK 465 GLY D 0 REMARK 465 GLY D 80 DBREF 36MB A -2 80 PDB 36MB 36MB -2 80 DBREF 36MB B -2 80 PDB 36MB 36MB -2 80 DBREF 36MB C -2 80 PDB 36MB 36MB -2 80 DBREF 36MB D -2 80 PDB 36MB 36MB -2 80 SEQRES 1 A 83 SER GLY GLY SER GLU GLU GLU ARG LYS ARG GLU ILE LEU SEQRES 2 A 83 LYS LEU TYR LEU GLU CYS VAL LEU LYS ASN LYS ASP LEU SEQRES 3 A 83 PRO PRO MET GLU ARG MET VAL VAL CYS GLN MET LYS VAL SEQRES 4 A 83 ASN GLU LYS TYR PRO ASP VAL THR ILE GLY GLU LEU ILE SEQRES 5 A 83 GLU VAL SER LYS GLU VAL GLU GLU LEU VAL LYS LYS GLY SEQRES 6 A 83 LEU GLU ALA VAL LYS LYS LYS LEU GLU GLU LEU GLU ASN SEQRES 7 A 83 LEU TYR PHE GLN GLY SEQRES 1 B 83 SER GLY GLY SER GLU GLU GLU ARG LYS ARG GLU ILE LEU SEQRES 2 B 83 LYS LEU TYR LEU GLU CYS VAL LEU LYS ASN LYS ASP LEU SEQRES 3 B 83 PRO PRO MET GLU ARG MET VAL VAL CYS GLN MET LYS VAL SEQRES 4 B 83 ASN GLU LYS TYR PRO ASP VAL THR ILE GLY GLU LEU ILE SEQRES 5 B 83 GLU VAL SER LYS GLU VAL GLU GLU LEU VAL LYS LYS GLY SEQRES 6 B 83 LEU GLU ALA VAL LYS LYS LYS LEU GLU GLU LEU GLU ASN SEQRES 7 B 83 LEU TYR PHE GLN GLY SEQRES 1 C 83 SER GLY GLY SER GLU GLU GLU ARG LYS ARG GLU ILE LEU SEQRES 2 C 83 LYS LEU TYR LEU GLU CYS VAL LEU LYS ASN LYS ASP LEU SEQRES 3 C 83 PRO PRO MET GLU ARG MET VAL VAL CYS GLN MET LYS VAL SEQRES 4 C 83 ASN GLU LYS TYR PRO ASP VAL THR ILE GLY GLU LEU ILE SEQRES 5 C 83 GLU VAL SER LYS GLU VAL GLU GLU LEU VAL LYS LYS GLY SEQRES 6 C 83 LEU GLU ALA VAL LYS LYS LYS LEU GLU GLU LEU GLU ASN SEQRES 7 C 83 LEU TYR PHE GLN GLY SEQRES 1 D 83 SER GLY GLY SER GLU GLU GLU ARG LYS ARG GLU ILE LEU SEQRES 2 D 83 LYS LEU TYR LEU GLU CYS VAL LEU LYS ASN LYS ASP LEU SEQRES 3 D 83 PRO PRO MET GLU ARG MET VAL VAL CYS GLN MET LYS VAL SEQRES 4 D 83 ASN GLU LYS TYR PRO ASP VAL THR ILE GLY GLU LEU ILE SEQRES 5 D 83 GLU VAL SER LYS GLU VAL GLU GLU LEU VAL LYS LYS GLY SEQRES 6 D 83 LEU GLU ALA VAL LYS LYS LYS LEU GLU GLU LEU GLU ASN SEQRES 7 D 83 LEU TYR PHE GLN GLY HET SO4 A 101 5 HET PRO A 102 8 HET SO4 D 101 5 HETNAM SO4 SULFATE ION HETNAM PRO PROLINE FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 PRO C5 H9 N O2 FORMUL 8 HOH *74(H2 O) HELIX 1 AA1 SER A 1 ASN A 20 1 20 HELIX 2 AA2 PRO A 24 TYR A 40 1 17 HELIX 3 AA3 THR A 44 LYS A 60 1 17 HELIX 4 AA4 GLY A 62 LEU A 76 1 15 HELIX 5 AA5 GLU B 2 ASN B 20 1 19 HELIX 6 AA6 PRO B 24 TYR B 40 1 17 HELIX 7 AA7 THR B 44 GLY B 62 1 19 HELIX 8 AA8 GLY B 62 ASN B 75 1 14 HELIX 9 AA9 GLU C 2 ASN C 20 1 19 HELIX 10 AB1 PRO C 24 TYR C 40 1 17 HELIX 11 AB2 THR C 44 GLY C 62 1 19 HELIX 12 AB3 GLY C 62 GLU C 74 1 13 HELIX 13 AB4 GLU D 2 ASN D 20 1 19 HELIX 14 AB5 PRO D 24 TYR D 40 1 17 HELIX 15 AB6 THR D 44 LYS D 61 1 18 HELIX 16 AB7 GLY D 62 TYR D 77 1 16 SSBOND 1 CYS A 16 CYS A 32 1555 1555 2.03 SSBOND 2 CYS B 16 CYS B 32 1555 1555 2.04 SSBOND 3 CYS C 16 CYS C 32 1555 1555 2.04 SSBOND 4 CYS D 16 CYS D 32 1555 1555 2.03 CRYST1 55.306 51.306 56.008 90.00 90.95 90.00 P 1 21 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 0.018081 0.000000 0.000300 0.00000 SCALE2 0.000000 0.019491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017857 0.00000 CONECT 141 268 CONECT 268 141 CONECT 801 928 CONECT 928 801 CONECT 1447 1574 CONECT 1574 1447 CONECT 2070 2197 CONECT 2197 2070 CONECT 2590 2591 2592 2593 2594 CONECT 2591 2590 CONECT 2592 2590 CONECT 2593 2590 CONECT 2594 2590 CONECT 2603 2604 2605 2606 2607 CONECT 2604 2603 CONECT 2605 2603 CONECT 2606 2603 CONECT 2607 2603 MASTER 255 0 3 16 0 0 0 6 2667 4 18 28 END