HEADER ANTIFUNGAL PROTEIN 07-AUG-18 6HA4 TITLE CRYSTAL STRUCTURE OF PAF - P-SULFONATOCALIX[4]ARENE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PC24G00380 PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM RUBENS (STRAIN ATCC 28089 / DSM SOURCE 3 1075 / NRRL 1951 / 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 06-NOV-24 6HA4 1 REMARK REVDAT 3 17-JAN-24 6HA4 1 REMARK REVDAT 2 27-MAR-19 6HA4 1 JRNL REVDAT 1 13-FEB-19 6HA4 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. 1.33 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 10142 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 526 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) : 1.33 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.48 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.77 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2679 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2089 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2546 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE : 0.2254 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.96 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 : 54 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.24380 REMARK 3 B22 (A**2) : -5.40360 REMARK 3 B33 (A**2) : 3.15970 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.71800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.180 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.071 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.072 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.076 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.069 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 : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 972 ; 6.000 ; HARMONIC REMARK 3 BOND ANGLES : 1759 ; 6.000 ; HARMONIC REMARK 3 TORSION ANGLES : 230 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 153 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 972 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 64 ; 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 : 1154 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.74 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.90 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.43 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): -3.7966 4.5228 31.3802 REMARK 3 T TENSOR REMARK 3 T11: -0.0129 T22: -0.0297 REMARK 3 T33: -0.0202 T12: 0.0070 REMARK 3 T13: -0.0213 T23: -0.0182 REMARK 3 L TENSOR REMARK 3 L11: 1.1555 L22: 0.7064 REMARK 3 L33: 1.1753 L12: -0.1822 REMARK 3 L13: 0.0215 L23: -0.2874 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: 0.0048 S13: -0.0542 REMARK 3 S21: -0.0008 S22: -0.0700 S23: 0.0213 REMARK 3 S31: -0.0123 S32: -0.0299 S33: 0.0452 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-16 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10142 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 27.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 2MHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 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 18.79350 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: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T3Y A 202 DBREF 6HA4 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 GOL A 201 6 HET T3Y A 202 48 HETNAM GOL GLYCEROL HETNAM T3Y 25,26,27,28-TETRAHYDROXYPENTACYCLO[19.3.1.1~3,7~.1~9, HETNAM 2 T3Y 13~.1~15,19~]OCTACOSA-1(25),3(28),4,6,9(27),10,12, HETNAM 3 T3Y 15(26),16,18,21,23-DODECAENE-5,11,17,23-TETRASULFONIC HETNAM 4 T3Y ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN T3Y 5,11,17,23-TETRA-SULPHONATO-CALIX[4]ARENE-25,26,27,28- HETSYN 2 T3Y TETROL FORMUL 2 GOL C3 H8 O3 FORMUL 3 T3Y C28 H24 O16 S4 FORMUL 4 HOH *55(H2 O) HELIX 1 AA1 PHE A 31 LYS A 35 5 5 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 ASN A 41 ASP A 46 -1 O VAL A 45 N TYR A 3 SHEET 5 AA1 5 VAL A 52 CYS A 54 -1 O ASP A 53 N THR A 44 SSBOND 1 CYS A 7 CYS A 36 1555 1555 2.04 SSBOND 2 CYS A 14 CYS A 43 1555 1555 2.03 SSBOND 3 CYS A 28 CYS A 54 1555 1555 2.03 SITE 1 AC1 7 SER A 10 ASN A 12 ASP A 19 ALA A 20 SITE 2 AC1 7 LYS A 27 HOH A 305 HOH A 312 SITE 1 AC2 16 ALA A 1 THR A 4 LYS A 6 LYS A 17 SITE 2 AC2 16 PRO A 29 LYS A 30 PHE A 31 ASP A 32 SITE 3 AC2 16 LYS A 35 THR A 47 HOH A 302 HOH A 303 SITE 4 AC2 16 HOH A 304 HOH A 319 HOH A 339 HOH A 344 CRYST1 22.719 37.587 29.956 90.00 111.75 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 0.044016 0.000000 0.017561 0.00000 SCALE2 0.000000 0.026605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035941 0.00000