HEADER ANTIMICROBIAL PROTEIN 09-APR-26 12KN TITLE SUPRAMOLECULAR ASSEMBLY OF A STAPHYLOCOCCAL DELTA-TOXIN PEPTIDE TITLE 2 FRAGMENT, STIP3-G3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMP; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AURICULARIS; SOURCE 4 ORGANISM_TAXID: 29379 KEYWDS ANTIMICROBIAL PEPTIDE, DELTA TOXIN, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.DEEYAGAHAGE,P.DHINDWAL,T.M.BONIECKI,A.RUZZINI REVDAT 1 14-OCT-26 12KN 0 JRNL AUTH K.DEEYAGAHAGE,P.DHINDWAL,M.T.BONIECKI,A.RUZZINI JRNL TITL SUPRAMOLECULAR ASSEMBLY OF AN ANTIMICROBIAL PEPTIDE INTO A JRNL TITL 2 PORE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. 22225 2026 JRNL REFN ESSN 1521-3773 JRNL PMID 42815953 JRNL DOI 10.1002/ANIE.2822225 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 3692 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 368 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 3.4500 - 2.7400 1.00 1100 122 0.2261 0.2757 REMARK 3 2 2.7400 - 2.4000 1.00 1078 120 0.2352 0.2957 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 548 REMARK 3 ANGLE : 0.408 744 REMARK 3 CHIRALITY : 0.035 98 REMARK 3 PLANARITY : 0.002 82 REMARK 3 DIHEDRAL : 12.215 181 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 101) REMARK 3 ORIGIN FOR THE GROUP (A): 5.9780 16.5978 11.6341 REMARK 3 T TENSOR REMARK 3 T11: 0.4693 T22: 0.2167 REMARK 3 T33: 0.3150 T12: -0.0952 REMARK 3 T13: -0.0147 T23: -0.0581 REMARK 3 L TENSOR REMARK 3 L11: 9.0780 L22: 7.7119 REMARK 3 L33: 7.3682 L12: 1.0046 REMARK 3 L13: 0.8965 L23: -4.3720 REMARK 3 S TENSOR REMARK 3 S11: 0.1535 S12: -0.1074 S13: 0.0519 REMARK 3 S21: -0.0235 S22: 0.1031 S23: 0.9974 REMARK 3 S31: 0.0484 S32: -1.8038 S33: 0.1563 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 17) REMARK 3 ORIGIN FOR THE GROUP (A): 14.6349 9.9537 12.1473 REMARK 3 T TENSOR REMARK 3 T11: 0.7691 T22: 0.2828 REMARK 3 T33: 0.4827 T12: -0.0108 REMARK 3 T13: 0.1046 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 7.6548 L22: 8.0956 REMARK 3 L33: 2.1957 L12: 2.8231 REMARK 3 L13: 3.0584 L23: 3.6663 REMARK 3 S TENSOR REMARK 3 S11: -0.1815 S12: 0.7892 S13: -0.5652 REMARK 3 S21: -0.4178 S22: 0.4576 S23: -0.9893 REMARK 3 S31: 1.0276 S32: 0.4319 S33: -0.3095 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 17) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5764 1.7151 13.8831 REMARK 3 T TENSOR REMARK 3 T11: 0.6734 T22: 0.3185 REMARK 3 T33: 0.4476 T12: -0.1299 REMARK 3 T13: -0.0036 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 7.1573 L22: 8.7681 REMARK 3 L33: 9.5829 L12: 5.1718 REMARK 3 L13: 6.6178 L23: 7.6016 REMARK 3 S TENSOR REMARK 3 S11: 0.3405 S12: -0.0442 S13: -0.3359 REMARK 3 S21: 0.8277 S22: -0.1869 S23: -0.8771 REMARK 3 S31: 1.4929 S32: 0.3425 S33: 0.0558 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 17) REMARK 3 ORIGIN FOR THE GROUP (A): 0.4414 8.6553 12.1444 REMARK 3 T TENSOR REMARK 3 T11: 0.8151 T22: 0.2377 REMARK 3 T33: 0.3858 T12: -0.1862 REMARK 3 T13: 0.0379 T23: -0.0454 REMARK 3 L TENSOR REMARK 3 L11: 7.7032 L22: 8.7748 REMARK 3 L33: 9.3021 L12: -1.4137 REMARK 3 L13: 0.6858 L23: -2.9058 REMARK 3 S TENSOR REMARK 3 S11: 0.1338 S12: -0.4817 S13: 0.1465 REMARK 3 S21: -0.2101 S22: 0.3979 S23: 0.1075 REMARK 3 S31: -1.0060 S32: -1.1235 S33: -0.3990 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 12KN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000306321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6852 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 38.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.10590 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL 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 (%): 58.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 20% ISOPROPANOL, REMARK 280 20% PEG 4000, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.46600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 50.57450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.46600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.57450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.46600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.57450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.46600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.57450 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 50.57450 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 50.57450 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 50.57450 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 50.57450 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 38.46600 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 38.46600 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 38.46600 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 23.06750 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 38.46600 REMARK 290 SMTRY3 16 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 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 LYS A 14 CE NZ REMARK 470 LYS B 7 CE NZ REMARK 470 LYS B 14 CD CE NZ REMARK 470 LYS B 15 CE NZ REMARK 470 LYS C 14 CE NZ DBREF 12KN A 1 17 PDB 12KN 12KN 1 17 DBREF 12KN B 1 17 PDB 12KN 12KN 1 17 DBREF 12KN C 1 17 PDB 12KN 12KN 1 17 DBREF 12KN D 1 17 PDB 12KN 12KN 1 17 SEQRES 1 A 17 THR VAL ALA GLY LEU VAL LYS TRP ILE LEU ASP THR VAL SEQRES 2 A 17 LYS LYS PHE ALA SEQRES 1 B 17 THR VAL ALA GLY LEU VAL LYS TRP ILE LEU ASP THR VAL SEQRES 2 B 17 LYS LYS PHE ALA SEQRES 1 C 17 THR VAL ALA GLY LEU VAL LYS TRP ILE LEU ASP THR VAL SEQRES 2 C 17 LYS LYS PHE ALA SEQRES 1 D 17 THR VAL ALA GLY LEU VAL LYS TRP ILE LEU ASP THR VAL SEQRES 2 D 17 LYS LYS PHE ALA HET EDO A 101 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *17(H2 O) HELIX 1 AA1 THR A 1 ALA A 17 1 17 HELIX 2 AA2 VAL B 2 ALA B 17 1 16 HELIX 3 AA3 VAL C 2 ALA C 17 1 16 HELIX 4 AA4 GLY D 4 ALA D 17 1 14 CRYST1 46.135 76.932 101.149 90.00 90.00 90.00 F 2 2 2 64 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 0.021676 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012998 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009886 0.00000 CONECT 530 531 532 CONECT 531 530 CONECT 532 530 533 CONECT 533 532 MASTER 313 0 1 4 0 0 0 6 546 4 4 8 END