HEADER APOPTOSIS 17-JUN-26 36LY TITLE CRYSTAL STRUCTURE OF MINI-BINDER MB07 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MB07; COMPND 3 CHAIN: A, B; 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 36LY 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. 2.55 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 4559 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 456 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 32.9700 - 3.7000 0.97 1380 153 0.2027 0.2639 REMARK 3 2 3.6600 - 2.9200 0.95 1352 155 0.2384 0.2799 REMARK 3 3 2.9200 - 2.5500 0.94 1371 148 0.2573 0.3440 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) : 0.378 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.569 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.42 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 1290 REMARK 3 ANGLE : 0.515 1728 REMARK 3 CHIRALITY : 0.035 196 REMARK 3 PLANARITY : 0.006 214 REMARK 3 DIHEDRAL : 19.126 534 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 36LY 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_1000309116. 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 : 4.5 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-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 : 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 : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4566 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 32.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 (%): 37.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE PH 4.5, AND 50 % W/V PEG 400, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SER A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 TYR A 77 REMARK 465 PHE A 78 REMARK 465 GLN A 79 REMARK 465 GLY A 80 REMARK 465 SER B -2 REMARK 465 GLY B -1 REMARK 465 GLY B 0 REMARK 465 TYR B 77 REMARK 465 PHE B 78 REMARK 465 GLN B 79 REMARK 465 GLY B 80 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 ASN A 20 34.45 -99.54 REMARK 500 GLU B 4 10.68 56.34 REMARK 500 ASN B 75 4.30 -68.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 36LY A -2 80 PDB 36LY 36LY -2 80 DBREF 36LY B -2 80 PDB 36LY 36LY -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 GLU VAL LEU LYS ASN LYS ASP LEU SEQRES 3 A 83 PRO PRO MET GLU ARG MET VAL VAL ALA 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 GLU VAL LEU LYS ASN LYS ASP LEU SEQRES 3 B 83 PRO PRO MET GLU ARG MET VAL VAL ALA 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 HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 A 103 5 HET SO4 A 104 5 HET SO4 A 105 5 HET SO4 A 106 5 HET SO4 B 101 5 HET SO4 B 102 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 8(O4 S 2-) FORMUL 11 HOH *3(H2 O) HELIX 1 AA1 GLU A 2 ASN A 20 1 19 HELIX 2 AA2 PRO A 24 TYR A 40 1 17 HELIX 3 AA3 THR A 44 LYS A 61 1 18 HELIX 4 AA4 GLY A 62 ASN A 75 1 14 HELIX 5 AA5 ARG B 5 ASN B 20 1 16 HELIX 6 AA6 PRO B 24 TYR B 40 1 17 HELIX 7 AA7 THR B 44 LYS B 61 1 18 HELIX 8 AA8 GLY B 62 LEU B 76 1 15 CRYST1 33.042 34.711 37.038 81.61 70.99 72.00 P 1 2 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 0.030265 -0.009832 -0.009948 0.00000 SCALE2 0.000000 0.030292 -0.001524 0.00000 SCALE3 0.000000 0.000000 0.028594 0.00000 CONECT 1251 1252 1253 1254 1255 CONECT 1252 1251 CONECT 1253 1251 CONECT 1254 1251 CONECT 1255 1251 CONECT 1256 1257 1258 1259 1260 CONECT 1257 1256 CONECT 1258 1256 CONECT 1259 1256 CONECT 1260 1256 CONECT 1261 1262 1263 1264 1265 CONECT 1262 1261 CONECT 1263 1261 CONECT 1264 1261 CONECT 1265 1261 CONECT 1266 1267 1268 1269 1270 CONECT 1267 1266 CONECT 1268 1266 CONECT 1269 1266 CONECT 1270 1266 CONECT 1271 1272 1273 1274 1275 CONECT 1272 1271 CONECT 1273 1271 CONECT 1274 1271 CONECT 1275 1271 CONECT 1276 1277 1278 1279 1280 CONECT 1277 1276 CONECT 1278 1276 CONECT 1279 1276 CONECT 1280 1276 CONECT 1281 1282 1283 1284 1285 CONECT 1282 1281 CONECT 1283 1281 CONECT 1284 1281 CONECT 1285 1281 CONECT 1286 1287 1288 1289 1290 CONECT 1287 1286 CONECT 1288 1286 CONECT 1289 1286 CONECT 1290 1286 MASTER 226 0 8 8 0 0 0 6 1291 2 40 14 END