HEADER ANTIFUNGAL PROTEIN 15-DEC-20 7BAF TITLE CRYSTAL STRUCTURE OF PAFB IN COMPLEX WITH ZINC COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIFUNGAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES 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; SOURCE 5 STRAIN: ATCC 28089 / DSM 1075 / NRRL 1951 / WISCONSIN 54-1255; SOURCE 6 GENE: AFP, PC12G08290; SOURCE 7 EXPRESSION_SYSTEM: PENICILLIUM RUBENS WISCONSIN 54-1255; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 500485 KEYWDS PENICILLIUM CHRYSOGENUM ANTIFUNGAL PROTEIN B, CALIX[N]ARENE, ZINC, KEYWDS 2 POROUS FRAMEWORK, MOLECULAR RECOGNITION, ANTIFUNGAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.GUAGNINI,A.HUBER,J.M.ALEX,F.MARX,P.B.CROWLEY REVDAT 3 31-JAN-24 7BAF 1 REMARK REVDAT 2 24-MAR-21 7BAF 1 JRNL REVDAT 1 17-MAR-21 7BAF 0 JRNL AUTH F.GUAGNINI,A.HUBER,J.M.ALEX,F.MARX,P.B.CROWLEY JRNL TITL POROUS ASSEMBLY OF AN ANTIFUNGAL PROTEIN MEDIATED BY ZINC JRNL TITL 2 AND SULFONATO-CALIX[8]ARENE. JRNL REF J.STRUCT.BIOL. V. 213 07711 2021 JRNL REFN ESSN 1095-8657 JRNL PMID 33631304 JRNL DOI 10.1016/J.JSB.2021.107711 REMARK 2 REMARK 2 RESOLUTION. 1.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 (18-SEP-2020) 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19755 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 952 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.12 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.85 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 397 REMARK 3 BIN R VALUE (WORKING SET) : 0.2008 REMARK 3 BIN FREE R VALUE : 0.2352 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 24 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 444 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.36810 REMARK 3 B22 (A**2) : -1.36810 REMARK 3 B33 (A**2) : 2.73630 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.140 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.035 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.034 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.035 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.033 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 : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 477 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 638 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 165 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 84 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 471 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 55 ; 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 : 461 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.07 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.28 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 13.00 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): -1.7130 24.3568 11.5421 REMARK 3 T TENSOR REMARK 3 T11: -0.0084 T22: -0.0102 REMARK 3 T33: 0.0073 T12: 0.0088 REMARK 3 T13: 0.0005 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.0124 L22: 0.3464 REMARK 3 L33: 1.0528 L12: -0.1108 REMARK 3 L13: -0.2358 L23: -0.1921 REMARK 3 S TENSOR REMARK 3 S11: -0.0069 S12: -0.0078 S13: -0.0046 REMARK 3 S21: -0.0139 S22: 0.0453 S23: -0.0069 REMARK 3 S31: -0.0512 S32: -0.0192 S33: -0.0384 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS WERE FULLY REFINED WITH ZERO REMARK 3 OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REMARK 3 REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT REMARK 3 SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY REMARK 4 REMARK 4 7BAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292113049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.98013 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : POINTLESS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19859 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 28.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.16300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.01400 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: 6HAJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 25 % PEG 3350, REMARK 280 0.2 M NH4CH3COO, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 14.27500 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 28.55000 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: 1020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 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 LEU A -2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 51 O HOH A 201 1.99 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 107 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 5 OE1 REMARK 620 2 GLU A 5 OE2 57.5 REMARK 620 3 HIS A 22 ND1 68.7 71.6 REMARK 620 4 ACT A 102 O 60.0 68.2 8.7 REMARK 620 5 ACT A 104 OXT 67.8 73.4 2.7 8.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 10 ND1 REMARK 620 2 HIS A 40 NE2 70.3 REMARK 620 3 GLU A 42 OE2 77.5 8.5 REMARK 620 4 ACT A 101 OXT 77.3 8.1 8.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 108 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HIS A 47 NE2 54.8 REMARK 620 3 ACT A 103 O 105.5 156.8 REMARK 620 4 ACT A 105 O 156.5 116.3 86.6 REMARK 620 5 ACT A 105 OXT 102.0 91.8 105.5 54.9 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NC2 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE SAME PROTEIN DBREF 7BAF A -2 56 UNP B6GXZ8 AFP_PENRW 35 92 SEQRES 1 A 58 LEU SER LYS PHE GLY GLY GLU CYS SER LEU LYS HIS ASN SEQRES 2 A 58 THR CYS THR TYR LEU LYS GLY GLY LYS ASN HIS VAL VAL SEQRES 3 A 58 ASN CYS GLY SER ALA ALA ASN LYS LYS CYS LYS SER ASP SEQRES 4 A 58 ARG HIS HIS CYS GLU TYR ASP GLU HIS HIS LYS ARG VAL SEQRES 5 A 58 ASP CYS GLN THR PRO VAL HET ACT A 101 4 HET ACT A 102 4 HET ACT A 103 4 HET ACT A 104 7 HET ACT A 105 7 HET ZN A 106 1 HET ZN A 107 1 HET ZN A 108 1 HETNAM ACT ACETATE ION HETNAM ZN ZINC ION FORMUL 2 ACT 5(C2 H3 O2 1-) FORMUL 7 ZN 3(ZN 2+) FORMUL 10 HOH *48(H2 O) SHEET 1 AA1 5 LYS A 20 ASN A 25 0 SHEET 2 AA1 5 THR A 12 LYS A 17 -1 N CYS A 13 O VAL A 24 SHEET 3 AA1 5 LYS A 1 SER A 7 -1 N GLU A 5 O THR A 14 SHEET 4 AA1 5 HIS A 40 ASP A 44 -1 O TYR A 43 N PHE A 2 SHEET 5 AA1 5 ARG A 49 ASP A 51 -1 O ARG A 49 N ASP A 44 SSBOND 1 CYS A 6 CYS A 34 1555 1555 2.05 SSBOND 2 CYS A 13 CYS A 41 1555 1555 2.05 SSBOND 3 CYS A 26 CYS A 52 1555 1555 2.03 LINK OE1 GLU A 5 ZN ZN A 107 1555 3564 2.02 LINK OE2 GLU A 5 ZN ZN A 107 1555 3564 2.45 LINK ND1 HIS A 10 ZN ZN A 106 1555 1555 1.99 LINK ND1 HIS A 22 ZN ZN A 107 1555 1555 2.01 LINK NE2 HIS A 39 ZN ZN A 108 1555 1555 1.94 LINK NE2 HIS A 40 ZN ZN A 106 1555 3564 2.01 LINK OE2 GLU A 42 ZN ZN A 106 1555 3564 1.98 LINK NE2 HIS A 47 ZN ZN A 108 1555 2775 2.13 LINK OXT ACT A 101 ZN ZN A 106 1555 3564 2.02 LINK O ACT A 102 ZN ZN A 107 1555 1555 1.94 LINK O ACT A 103 ZN ZN A 108 1555 1555 1.99 LINK OXT ACT A 104 ZN ZN A 107 1555 1555 2.07 LINK O ACT A 105 ZN ZN A 108 1555 1555 2.67 LINK OXT ACT A 105 ZN ZN A 108 1555 1555 1.88 CRYST1 32.942 32.942 42.825 90.00 90.00 120.00 P 31 3 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 0.030356 0.017526 0.000000 0.00000 SCALE2 0.000000 0.035053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023351 0.00000