HEADER ANTIMICROBIAL PROTEIN 09-APR-26 12KO TITLE SUPRAMOLECULAR ASSEMBLY OF A STAPHYLOCOCCAL DELTA-TOXIN PEPTIDE TITLE 2 FRAGMENT, STIP3-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THR-VAL-GLY-GLY-LEU-VAL-LYS-TRP-ILE-LEU-ASP-THR-VAL-LYS- COMPND 3 LYS-PHE-ALA; COMPND 4 CHAIN: B, A, C; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AURICULARIS; SOURCE 4 ORGANISM_TAXID: 29379 KEYWDS ANTIMICROBIAL PEPTIDE, PORE, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.RUZZINI,P.DHINDWAL,T.M.BONIECKI REVDAT 1 14-OCT-26 12KO 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. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.1_5286: ???) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4809 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.790 REMARK 3 FREE R VALUE TEST SET COUNT : 471 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 2.4400 - 1.9400 1.00 1437 156 0.2087 0.2533 REMARK 3 2 1.9400 - 1.7000 1.00 1430 152 0.2390 0.2794 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.540 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 : 0.017 398 REMARK 3 ANGLE : 1.663 534 REMARK 3 CHIRALITY : 0.075 67 REMARK 3 PLANARITY : 0.007 58 REMARK 3 DIHEDRAL : 17.217 133 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 17) REMARK 3 ORIGIN FOR THE GROUP (A): -17.8432 -12.1887 -1.9812 REMARK 3 T TENSOR REMARK 3 T11: 0.1456 T22: 0.2265 REMARK 3 T33: 0.1208 T12: 0.0401 REMARK 3 T13: 0.0180 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 8.2572 L22: 7.0258 REMARK 3 L33: 7.4178 L12: -1.6674 REMARK 3 L13: 4.8387 L23: -1.7537 REMARK 3 S TENSOR REMARK 3 S11: 0.4062 S12: 0.4759 S13: -0.1424 REMARK 3 S21: -0.3706 S22: 0.0417 S23: 0.1650 REMARK 3 S31: -0.0598 S32: -0.0012 S33: -0.3887 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 17) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6097 -5.1201 4.8126 REMARK 3 T TENSOR REMARK 3 T11: 0.2444 T22: 0.1320 REMARK 3 T33: 0.1321 T12: -0.0149 REMARK 3 T13: -0.0093 T23: -0.0579 REMARK 3 L TENSOR REMARK 3 L11: 7.6970 L22: 8.4884 REMARK 3 L33: 6.7725 L12: 2.0239 REMARK 3 L13: -0.8880 L23: -3.6546 REMARK 3 S TENSOR REMARK 3 S11: -0.1246 S12: -0.1934 S13: 0.2339 REMARK 3 S21: 0.2452 S22: -0.0237 S23: 0.1752 REMARK 3 S31: -0.3315 S32: -0.2526 S33: 0.2090 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 2 THROUGH 16) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2648 -6.0703 4.3569 REMARK 3 T TENSOR REMARK 3 T11: 0.4139 T22: 0.4328 REMARK 3 T33: 1.1661 T12: -0.1054 REMARK 3 T13: 0.0007 T23: -0.0975 REMARK 3 L TENSOR REMARK 3 L11: 3.1427 L22: 3.7894 REMARK 3 L33: 7.0934 L12: -0.8908 REMARK 3 L13: 3.6574 L23: 1.2404 REMARK 3 S TENSOR REMARK 3 S11: -0.6911 S12: -0.1974 S13: 1.1846 REMARK 3 S21: 0.1634 S22: -0.1411 S23: -0.6988 REMARK 3 S31: -0.6699 S32: 0.7088 S33: 0.6980 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 12KO 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_1000306127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.18 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 43.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.02707 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 63.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07625 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 (%): 35.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE, 15% ISO-PROPANOL REMARK 280 (V/V) 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.06667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.03333 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 15.05000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 5.01667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.08333 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, 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 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 5.01667 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 THR C 1 REMARK 465 ALA C 17 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 B 14 CD CE NZ REMARK 470 LYS A 14 CD CE NZ REMARK 470 LYS C 14 CG CD CE NZ REMARK 470 PHE C 16 CG CD1 CD2 CE1 CE2 CZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS C 15 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CG2 THR B 1 C3 IPA A 101 3445 1.63 REMARK 500 REMARK 500 REMARK: NULL 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 LEU C 5 -56.48 -155.80 REMARK 500 VAL C 6 -46.36 57.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 12KO B 1 17 PDB 12KO 12KO 1 17 DBREF 12KO A 1 17 PDB 12KO 12KO 1 17 DBREF 12KO C 1 17 PDB 12KO 12KO 1 17 SEQRES 1 B 17 THR VAL GLY GLY LEU VAL LYS TRP ILE LEU ASP THR VAL SEQRES 2 B 17 LYS LYS PHE ALA SEQRES 1 A 17 THR VAL GLY GLY LEU VAL LYS TRP ILE LEU ASP THR VAL SEQRES 2 A 17 LYS LYS PHE ALA SEQRES 1 C 17 THR VAL GLY GLY LEU VAL LYS TRP ILE LEU ASP THR VAL SEQRES 2 C 17 LYS LYS PHE ALA HET IPA A 101 4 HET TOE A 102 11 HET IPA A 103 4 HETNAM IPA ISOPROPYL ALCOHOL HETNAM TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL HETSYN IPA 2-PROPANOL FORMUL 4 IPA 2(C3 H8 O) FORMUL 5 TOE C7 H16 O4 FORMUL 7 HOH *15(H2 O) HELIX 1 AA1 THR B 1 ALA B 17 1 17 HELIX 2 AA2 VAL A 2 ALA A 17 1 16 HELIX 3 AA3 VAL C 6 PHE C 16 1 11 CRYST1 49.748 49.748 30.100 90.00 90.00 120.00 P 65 18 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 0.020101 0.011605 0.000000 0.00000 SCALE2 0.000000 0.023211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033223 0.00000 CONECT 380 381 CONECT 381 380 382 383 CONECT 382 381 CONECT 383 381 CONECT 384 385 CONECT 385 384 386 CONECT 386 385 387 CONECT 387 386 388 CONECT 388 387 389 CONECT 389 388 390 CONECT 390 389 391 CONECT 391 390 392 CONECT 392 391 393 CONECT 393 392 394 CONECT 394 393 CONECT 395 396 CONECT 396 395 397 398 CONECT 397 396 CONECT 398 396 MASTER 310 0 3 3 0 0 0 6 404 3 19 6 END