HEADER ANTIFUNGAL PROTEIN 07-AUG-18 6HAH TITLE CRYSTAL STRUCTURE OF PAF - P-SULFONATOCALIX[6]ARENE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PC24G00380 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: PENICILLIUM RUBENS WISCONSIN 54-1255; SOURCE 4 ORGANISM_TAXID: 500485 KEYWDS PENICILLIUM CHRYSOGENUM, ANTIFUNGAL PROTEIN, CALIXARENE, MOLECULAR KEYWDS 2 GLUES, NUCLEATING AGENT EXPDTA X-RAY DIFFRACTION AUTHOR J.M.ALEX,M.RENNIE,S.ENGILBERGE,G.BATTA,P.B.CROWLEY REVDAT 4 23-OCT-24 6HAH 1 REMARK REVDAT 3 01-MAY-24 6HAH 1 REMARK REVDAT 2 27-MAR-19 6HAH 1 JRNL REVDAT 1 13-FEB-19 6HAH 0 JRNL AUTH J.M.ALEX,M.L.RENNIE,S.ENGILBERGE,G.LEHOCZKI,H.DOROTTYA, JRNL AUTH 2 A.FIZIL,G.BATTA,P.B.CROWLEY JRNL TITL CALIXARENE-MEDIATED ASSEMBLY OF A SMALL ANTIFUNGAL PROTEIN. JRNL REF IUCRJ V. 6 238 2019 JRNL REFN ESSN 2052-2525 JRNL PMID 30867921 JRNL DOI 10.1107/S2052252519000411 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 8576 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 440 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.62 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.53 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2384 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2065 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2251 REMARK 3 BIN R VALUE (WORKING SET) : 0.2043 REMARK 3 BIN FREE R VALUE : 0.2405 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.58 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 133 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 433 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.73070 REMARK 3 B22 (A**2) : -0.98530 REMARK 3 B33 (A**2) : 2.71600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.80920 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.200 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.097 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.095 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.108 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.091 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 993 ; 6.000 ; HARMONIC REMARK 3 BOND ANGLES : 1776 ; 6.000 ; HARMONIC REMARK 3 TORSION ANGLES : 236 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 151 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 993 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 62 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1175 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 5.36 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.48 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 12.4659 7.7242 37.7892 REMARK 3 T TENSOR REMARK 3 T11: -0.0226 T22: -0.0047 REMARK 3 T33: -0.0152 T12: -0.0093 REMARK 3 T13: -0.0254 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 2.5255 L22: 9.4775 REMARK 3 L33: 3.8355 L12: 2.9490 REMARK 3 L13: -0.6422 L23: -1.4472 REMARK 3 S TENSOR REMARK 3 S11: -0.1803 S12: -0.0181 S13: -0.0198 REMARK 3 S21: -0.4821 S22: 0.1560 S23: 0.0334 REMARK 3 S31: 0.1075 S32: 0.0473 S33: 0.0242 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HAH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-17 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8592 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 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: PAF-P-SULFONATOCALIX[4]ARENE STRUCTURE (BUT DEVOID REMARK 200 OF THE P-SULFONATOCALIX[4]ARENE) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350 + 0.05 M SODIUM ACETATE REMARK 280 PH 5.6, VAPOR DIFFUSION, HANGING 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 19.29500 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 33 O REMARK 620 2 ASP A 53 OD1 94.1 REMARK 620 3 CYS A 54 O 94.4 84.6 REMARK 620 4 ASP A 55 OD1 165.1 100.5 84.0 REMARK 620 5 HOH A 214 O 90.0 81.3 165.6 95.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FWQ A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FWN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HA4 RELATED DB: PDB REMARK 900 6HA4 CONTAINS THE SAME PROTEIN COMPLEXED WITH SULFONATOCALIX[6]ARENE DBREF 6HAH A 1 55 UNP B6HWK0 B6HWK0_PENRW 38 92 SEQRES 1 A 55 ALA LYS TYR THR GLY LYS CYS THR LYS SER LYS ASN GLU SEQRES 2 A 55 CYS LYS TYR LYS ASN ASP ALA GLY LYS ASP THR PHE ILE SEQRES 3 A 55 LYS CYS PRO LYS PHE ASP ASN LYS LYS CYS THR LYS ASP SEQRES 4 A 55 ASN ASN LYS CYS THR VAL ASP THR TYR ASN ASN ALA VAL SEQRES 5 A 55 ASP CYS ASP HET FWQ A 101 72 HET FWN A 102 12 HET GOL A 103 6 HET NA A 104 1 HETNAM FWQ P-SULFONATOCALIX[6]ARENE HETNAM FWN 2-[2-(2-ETHOXYETHOXY)ETHOXY]ETHANOL HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FWQ C42 H30 O24 S6 6- FORMUL 3 FWN C8 H18 O4 FORMUL 4 GOL C3 H8 O3 FORMUL 5 NA NA 1+ FORMUL 6 HOH *55(H2 O) SHEET 1 AA1 5 ASP A 23 LYS A 27 0 SHEET 2 AA1 5 GLU A 13 LYS A 17 -1 N CYS A 14 O ILE A 26 SHEET 3 AA1 5 LYS A 2 THR A 8 -1 N LYS A 6 O LYS A 15 SHEET 4 AA1 5 LYS A 42 ASP A 46 -1 O CYS A 43 N GLY A 5 SHEET 5 AA1 5 ALA A 51 CYS A 54 -1 O ALA A 51 N ASP A 46 SSBOND 1 CYS A 7 CYS A 36 1555 1555 2.05 SSBOND 2 CYS A 14 CYS A 43 1555 1555 2.05 SSBOND 3 CYS A 28 CYS A 54 1555 1555 2.03 LINK O ASN A 33 NA NA A 104 1555 1555 2.61 LINK OD1 ASP A 53 NA NA A 104 1555 1555 2.31 LINK O CYS A 54 NA NA A 104 1555 1555 2.28 LINK OD1 ASP A 55 NA NA A 104 1555 1555 2.55 LINK NA NA A 104 O HOH A 214 1555 2748 2.24 SITE 1 AC1 23 THR A 4 LYS A 6 LYS A 9 LYS A 17 SITE 2 AC1 23 LYS A 27 CYS A 28 PRO A 29 LYS A 30 SITE 3 AC1 23 PHE A 31 LYS A 34 LYS A 38 LYS A 42 SITE 4 AC1 23 TYR A 48 VAL A 52 FWN A 102 HOH A 201 SITE 5 AC1 23 HOH A 204 HOH A 205 HOH A 207 HOH A 213 SITE 6 AC1 23 HOH A 225 HOH A 228 HOH A 229 SITE 1 AC2 4 LYS A 9 LYS A 17 ASN A 18 FWQ A 101 SITE 1 AC3 7 LYS A 6 LYS A 15 TYR A 16 LYS A 17 SITE 2 AC3 7 ASP A 23 HOH A 214 HOH A 242 SITE 1 AC4 4 ASN A 33 ASP A 53 CYS A 54 ASP A 55 CRYST1 24.739 38.590 29.230 90.00 112.09 90.00 P 1 21 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 0.040422 0.000000 0.016405 0.00000 SCALE2 0.000000 0.025913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036922 0.00000