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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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