HEADER ANTIMICROBIAL PROTEIN 13-DEC-24 9HPP TITLE HELICAL FORM OF CITROPIN 1.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CITROPIN-1.3; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: RANOIDEA CITROPA; SOURCE 4 ORGANISM_COMMON: BLUE MOUNTAINS TREEFROG; SOURCE 5 ORGANISM_TAXID: 94770 KEYWDS FROG, FIBRIL, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.BLOCH,B.RAYAN,M.LANDAU REVDAT 2 24-DEC-25 9HPP 1 JRNL REVDAT 1 08-OCT-25 9HPP 0 JRNL AUTH F.STRATI,M.P.CALI,Y.BLOCH,S.MOSTAFAVI,J.MONISTROL,A.GOLUBEV, JRNL AUTH 2 B.RAYAN,E.GUSTAVSSON,M.LANDAU JRNL TITL STRUCTURAL AND FUNCTIONAL VERSATILITY OF THE AMYLOIDOGENIC JRNL TITL 2 NON-AMIDATED VARIANT OF THE ANTIMICROBIAL PEPTIDE CITROPIN JRNL TITL 3 1.3. JRNL REF ADV SCI V. 12 03997 2025 JRNL REFN ESSN 2198-3844 JRNL PMID 41016026 JRNL DOI 10.1002/ADVS.202503997 REMARK 2 REMARK 2 RESOLUTION. 1.56 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 7856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.288 REMARK 3 R VALUE (WORKING SET) : 0.284 REMARK 3 FREE R VALUE : 0.323 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 785 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 47.9600 - 2.8400 0.99 1304 145 0.2978 0.3500 REMARK 3 2 2.8400 - 2.2500 1.00 1216 136 0.2551 0.2602 REMARK 3 3 2.2500 - 1.9700 1.00 1189 130 0.2434 0.2877 REMARK 3 4 1.9700 - 1.7900 1.00 1175 131 0.2786 0.3072 REMARK 3 5 1.7900 - 1.6600 1.00 1171 130 0.2956 0.3627 REMARK 3 6 1.6600 - 1.5600 0.87 1016 113 0.3761 0.3831 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) : 0.222 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.41 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 : 0.015 242 REMARK 3 ANGLE : 1.153 327 REMARK 3 CHIRALITY : 0.066 43 REMARK 3 PLANARITY : 0.007 39 REMARK 3 DIHEDRAL : 17.332 91 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 9HPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292143988. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 2.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20230630 REMARK 200 DATA SCALING SOFTWARE : XDS 20230630 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7919 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 47.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 9.560 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 47.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 43.35 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20%V/V GLYCEROL, 8%W/V PEG 8,000 AND REMARK 280 8%W/V PEG 1,000. PEPTIDE PREPARED IN 2M ACETATE., PH 2.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 3 2 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+3/4,X+1/4,-Z+1/4 REMARK 290 14555 -Y+3/4,-X+3/4,-Z+3/4 REMARK 290 15555 Y+1/4,-X+1/4,Z+3/4 REMARK 290 16555 -Y+1/4,X+3/4,Z+1/4 REMARK 290 17555 X+3/4,Z+1/4,-Y+1/4 REMARK 290 18555 -X+1/4,Z+3/4,Y+1/4 REMARK 290 19555 -X+3/4,-Z+3/4,-Y+3/4 REMARK 290 20555 X+1/4,-Z+1/4,Y+3/4 REMARK 290 21555 Z+3/4,Y+1/4,-X+1/4 REMARK 290 22555 Z+1/4,-Y+1/4,X+3/4 REMARK 290 23555 -Z+1/4,Y+3/4,X+1/4 REMARK 290 24555 -Z+3/4,-Y+3/4,-X+3/4 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 33.91500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.91500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.91500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.91500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.91500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 33.91500 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 33.91500 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 33.91500 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 33.91500 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 33.91500 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 33.91500 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 33.91500 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 33.91500 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 33.91500 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 33.91500 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 33.91500 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 33.91500 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 50.87250 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 16.95750 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 16.95750 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 50.87250 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 50.87250 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 50.87250 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 16.95750 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 16.95750 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 50.87250 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 16.95750 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 50.87250 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 16.95750 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 50.87250 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 16.95750 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 16.95750 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 16.95750 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 50.87250 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 16.95750 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 50.87250 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 50.87250 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 50.87250 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 16.95750 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 16.95750 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 50.87250 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 50.87250 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 16.95750 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 16.95750 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 16.95750 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 16.95750 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 50.87250 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 16.95750 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 50.87250 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 16.95750 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 50.87250 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 50.87250 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 50.87250 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 DBREF 9HPP A 1 16 UNP P81846 CT13_RANCI 1 16 DBREF 9HPP B 1 16 UNP P81846 CT13_RANCI 1 16 SEQRES 1 A 16 GLY LEU PHE ASP ILE ILE LYS LYS VAL ALA SER VAL ILE SEQRES 2 A 16 GLY GLY LEU SEQRES 1 B 16 GLY LEU PHE ASP ILE ILE LYS LYS VAL ALA SER VAL ILE SEQRES 2 B 16 GLY GLY LEU FORMUL 3 HOH *9(H2 O) HELIX 1 AA1 GLY A 1 LEU A 16 1 16 HELIX 2 AA2 LEU B 2 GLY B 15 1 14 CRYST1 67.830 67.830 67.830 90.00 90.00 90.00 P 41 3 2 48 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 0.014743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014743 0.00000 TER 263 LEU A 16 TER 520 LEU B 16 HETATM 521 O HOH A 101 15.196 3.897 3.831 1.00 46.78 O HETATM 522 O HOH A 102 19.447 0.880 -3.987 1.00 32.24 O HETATM 523 O HOH A 103 11.432 0.187 10.553 1.00 52.33 O HETATM 524 O HOH A 104 18.533 5.292 6.447 1.00 49.83 O HETATM 525 O HOH B 101 12.533 -5.098 16.787 1.00 34.28 O HETATM 526 O HOH B 102 15.063 2.190 1.640 1.00 47.94 O HETATM 527 O HOH B 103 15.063 -0.223 13.560 1.00 32.09 O HETATM 528 O HOH B 104 10.311 -9.225 16.981 1.00 29.59 O HETATM 529 O HOH B 105 18.031 3.838 8.054 1.00 36.71 O MASTER 273 0 0 2 0 0 0 6 239 2 0 4 END