HEADER LIPID BINDING PROTEIN 13-OCT-15 5E7X TITLE LIGAND BINDING DOMAIN 1 OF PENICILLIUM MARNEFFEI MP1 PROTEIN IN TITLE 2 COMPLEX WITH PALMITIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL WALL ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-181; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TALAROMYCES MARNEFFEI PM1; SOURCE 3 ORGANISM_TAXID: 1077442; SOURCE 4 GENE: GQ26_0022220; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: HIS-SUMO KEYWDS PALMITIC ACID, MP1, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.H.LAM,H.ZHANG,Q.HAO REVDAT 3 20-MAR-24 5E7X 1 REMARK REVDAT 2 06-MAR-19 5E7X 1 COMPND SOURCE JRNL REMARK REVDAT 2 2 1 DBREF HELIX SITE ATOM REVDAT 1 19-OCT-16 5E7X 0 JRNL AUTH W.H.LAM,K.H.SZE,Y.KE,M.K.TSE,H.ZHANG,P.C.Y.WOO,S.K.P.LAU, JRNL AUTH 2 C.C.Y.LAU,S.XU,P.M.LAI,T.ZHOU,S.V.ANTONYUK,R.Y.T.KAO, JRNL AUTH 3 K.Y.YUEN,Q.HAO JRNL TITL TALAROMYCES MARNEFFEIMP1 PROTEIN, A NOVEL VIRULENCE FACTOR, JRNL TITL 2 CARRIES TWO ARACHIDONIC ACID-BINDING DOMAINS TO SUPPRESS JRNL TITL 3 INFLAMMATORY RESPONSES IN HOSTS. JRNL REF INFECT. IMMUN. 2019 JRNL REFN ESSN 1098-5522 JRNL PMID 30670555 JRNL DOI 10.1128/IAI.00679-18 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 13818 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 733 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1151 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -1.17000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5E7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 38.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.51800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.5 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 12000, SODIUM ACETATE, AMMONIUM REMARK 280 SULPHATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.84500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.26750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.42250 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: 8180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 PLM A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CSD RELATED DB: PDB DBREF1 5E7X A 27 181 UNP A0A093VKV7_TALMA DBREF2 5E7X A A0A093VKV7 27 181 SEQRES 1 A 155 THR LYS ASP GLN ARG ASP VAL ASN VAL PHE LYS LYS VAL SEQRES 2 A 155 LEU GLU ASN ILE GLY ASN ALA VAL THR GLN PHE ASN ASN SEQRES 3 A 155 ASP ILE LEU ALA TYR THR GLY GLY ASP ALA ASN HIS LEU SEQRES 4 A 155 ILE HIS ASP GLY ASP ALA ILE ILE LYS ALA THR GLU ASN SEQRES 5 A 155 GLY LEU GLN GLU LEU GLY PRO GLN PRO PRO LEU SER LEU SEQRES 6 A 155 THR GLU ALA LEU ALA LEU VAL GLY PRO VAL GLN GLY VAL SEQRES 7 A 155 ASN LYS LEU ILE MET LYS THR VAL ASP HIS LEU ILE GLU SEQRES 8 A 155 LYS LYS GLY PRO LEU VAL GLY GLY GLY TYR GLY PRO GLN SEQRES 9 A 155 VAL LYS ALA SER LEU GLN LYS GLN ALA HIS ALA ALA VAL SEQRES 10 A 155 THR LEU SER GLU LEU VAL SER SER LYS VAL PRO SER PRO SEQRES 11 A 155 LEU ALA PRO ILE SER LYS GLN LEU SER ASP GLN VAL ALA SEQRES 12 A 155 GLN ALA LEU GLN LYS GLY ILE GLU ALA PHE SER ILE HET PLM A 301 18 HET ACT A 302 4 HET GOL A 303 6 HETNAM PLM PALMITIC ACID HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PLM C16 H32 O2 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *66(H2 O) HELIX 1 AA1 THR A 27 TYR A 57 1 31 HELIX 2 AA2 ALA A 62 GLY A 84 1 23 HELIX 3 AA3 SER A 90 ALA A 96 1 7 HELIX 4 AA4 LEU A 97 GLU A 117 1 21 HELIX 5 AA5 LYS A 118 GLY A 125 1 8 HELIX 6 AA6 TYR A 127 VAL A 153 1 27 HELIX 7 AA7 PRO A 154 PRO A 156 5 3 HELIX 8 AA8 LEU A 157 PHE A 179 1 23 SITE 1 AC1 8 ILE A 72 ALA A 94 ILE A 108 GLN A 138 SITE 2 AC1 8 LEU A 157 SER A 165 LEU A 172 HOH A 416 SITE 1 AC2 3 LYS A 74 GLU A 77 ASN A 78 SITE 1 AC3 2 ASN A 78 HOH A 412 CRYST1 52.580 52.580 57.690 90.00 90.00 90.00 P 43 4 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 0.019019 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017334 0.00000