HEADER ANTIFUNGAL PROTEIN 12-MAY-03 1P9G TITLE CRYSTAL STRUCTURE OF A NOVEL ANTIFUNGAL PROTEIN DISTINCT WITH FIVE TITLE 2 DISULFIDE BRIDGES FROM ECOMMIA ULMOIDES OLIVER AT ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: EAFP 2; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EUCOMMIA ULMOIDES; SOURCE 3 ORGANISM_TAXID: 4392; SOURCE 4 TISSUE: TREE BARK KEYWDS ANTIFUNGAL PEPTIDE, ATOMIC RESOLUTION, ANTIFUNGAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIANG,R.H.HUANG,X.Z.LIU,D.C.WANG REVDAT 6 25-DEC-19 1P9G 1 SEQRES LINK REVDAT 5 11-OCT-17 1P9G 1 REMARK REVDAT 4 24-FEB-09 1P9G 1 VERSN REVDAT 3 05-OCT-04 1P9G 1 JRNL REVDAT 2 15-JUN-04 1P9G 1 SOURCE REVDAT 1 01-JUN-04 1P9G 0 JRNL AUTH Y.XIANG,R.H.HUANG,X.Z.LIU,Y.ZHANG,D.C.WANG JRNL TITL CRYSTAL STRUCTURE OF A NOVEL ANTIFUNGAL PROTEIN DISTINCT JRNL TITL 2 WITH FIVE DISULFIDE BRIDGES FROM EUCOMMIA ULMOIDES OLIVER AT JRNL TITL 3 AN ATOMIC RESOLUTION. JRNL REF J.STRUCT.BIOL. V. 148 86 2004 JRNL REFN ISSN 1047-8477 JRNL PMID 15363789 JRNL DOI 10.1016/J.JSB.2004.04.002 REMARK 2 REMARK 2 RESOLUTION. 0.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.068 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.068 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.079 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 885 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 22113 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.065 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.065 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.076 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 821 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 20593 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 282 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 345.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 249.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 7 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3401 REMARK 3 NUMBER OF RESTRAINTS : 3876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.033 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.150 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.142 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.008 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.032 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: CSD L-PYROGLUTAMIC ACID DATA FOR PCA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 5% REMARK 4 REMARK 4 1P9G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SILICON (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22113 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.840 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, ISO-PROPANOL, PH 5.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 11.58900 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 9 N - CA - CB ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 9 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 TYR A 20 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 SER A 25 N - CA - CB ANGL. DEV. = -9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 42 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 43 REMARK 999 REMARK 999 IT APPEARS THAT THIS PROTEIN SEQUENCE HAS NOT BEEN DEPOSITED IN REMARK 999 THE SEQUENCE DATABASE. DBREF 1P9G A 1 41 UNP P83597 EAP2_EUCUL 1 41 SEQRES 1 A 41 PCA THR CYS ALA SER ARG CYS PRO ARG PRO CYS ASN ALA SEQRES 2 A 41 GLY LEU CYS CYS SER ILE TYR GLY TYR CYS GLY SER GLY SEQRES 3 A 41 ALA ALA TYR CYS GLY ALA GLY ASN CYS ARG CYS GLN CYS SEQRES 4 A 41 ARG GLY MODRES 1P9G PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 14 HET ACT A 42 4 HET ACT A 43 4 HETNAM PCA PYROGLUTAMIC ACID HETNAM ACT ACETATE ION FORMUL 1 PCA C5 H7 N O3 FORMUL 2 ACT 2(C2 H3 O2 1-) FORMUL 4 HOH *61(H2 O) HELIX 1 1 THR A 2 CYS A 7 5 6 HELIX 2 2 GLY A 26 GLY A 31 1 6 SHEET 1 A 3 CYS A 23 GLY A 24 0 SHEET 2 A 3 CYS A 16 SER A 18 -1 N CYS A 16 O GLY A 24 SHEET 3 A 3 CYS A 35 CYS A 37 -1 O ARG A 36 N CYS A 17 SSBOND 1 CYS A 3 CYS A 17 1555 1555 2.03 SSBOND 2 CYS A 7 CYS A 37 1555 1555 2.03 SSBOND 3 CYS A 11 CYS A 23 1555 1555 2.03 SSBOND 4 CYS A 16 CYS A 30 1555 1555 2.03 SSBOND 5 CYS A 35 CYS A 39 1555 1555 2.02 LINK C PCA A 1 N THR A 2 1555 1555 1.30 CISPEP 1 CYS A 7 PRO A 8 0 17.57 SITE 1 AC1 8 PCA A 1 CYS A 3 ARG A 6 GLY A 21 SITE 2 AC1 8 TYR A 22 CYS A 23 HOH A 58 HOH A 71 SITE 1 AC2 5 ASN A 12 ALA A 13 ARG A 40 HOH A 53 SITE 2 AC2 5 HOH A 73 CRYST1 19.011 23.178 30.720 90.00 98.56 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 0.052601 0.000000 0.007918 0.00000 SCALE2 0.000000 0.043144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032919 0.00000 HETATM 1 N PCA A 1 3.193 -2.718 -10.373 1.00 7.34 N ANISOU 1 N PCA A 1 772 982 1036 -155 -112 -179 N HETATM 2 CA PCA A 1 3.156 -2.597 -11.784 1.00 6.61 C ANISOU 2 CA PCA A 1 692 775 1043 -95 98 -120 C HETATM 3 CB PCA A 1 4.602 -3.005 -12.187 1.00 10.33 C ANISOU 3 CB PCA A 1 694 1527 1702 -155 264 -376 C HETATM 4 CG PCA A 1 5.322 -3.219 -10.888 1.00 12.80 C ANISOU 4 CG PCA A 1 702 1383 2780 -146 -160 297 C HETATM 5 CD PCA A 1 4.367 -3.015 -9.854 1.00 9.85 C ANISOU 5 CD PCA A 1 983 1073 1686 -310 -419 197 C HETATM 6 OE PCA A 1 4.610 -3.104 -8.646 1.00 16.39 O ANISOU 6 OE PCA A 1 2121 2087 2019 -738 -1231 463 O HETATM 7 C PCA A 1 2.117 -3.462 -12.460 1.00 6.23 C ANISOU 7 C PCA A 1 657 853 856 56 95 -124 C HETATM 8 O PCA A 1 1.794 -3.162 -13.605 1.00 9.19 O ANISOU 8 O PCA A 1 1120 1567 805 -56 -85 77 O HETATM 9 H PCA A 1 2.493 -2.605 -9.886 1.00 8.81 H HETATM 10 HA PCA A 1 3.004 -1.660 -12.025 1.00 7.93 H HETATM 11 HB2 PCA A 1 4.595 -3.819 -12.714 1.00 12.39 H HETATM 12 HB3 PCA A 1 5.026 -2.302 -12.703 1.00 12.39 H HETATM 13 HG2 PCA A 1 5.680 -4.119 -10.844 1.00 15.36 H HETATM 14 HG3 PCA A 1 6.055 -2.590 -10.800 1.00 15.36 H