HEADER ANTIFUNGAL PROTEIN 29-AUG-97 1AUN TITLE PATHOGENESIS-RELATED PROTEIN 5D FROM NICOTIANA TABACUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PR-5D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OSMOTIN-LIKE PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NICOTIANA TABACUM; SOURCE 3 ORGANISM_COMMON: COMMON TOBACCO; SOURCE 4 ORGANISM_TAXID: 4097; SOURCE 5 STRAIN: SAMSUN NN; SOURCE 6 CELL: CULTURED CELL; SOURCE 7 CELLULAR_LOCATION: VACUOLE KEYWDS ANTIFUNGAL PROTEIN, PATHOGENESIS-RELATED PROTEIN, PR-5D, OSMOTIN, KEYWDS 2 THAUMATIN-LIKE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.KOIWA,H.KATO,T.NAKATSU,J.ODA,Y.YAMADA,F.SATO REVDAT 4 02-AUG-23 1AUN 1 REMARK REVDAT 3 24-FEB-09 1AUN 1 VERSN REVDAT 2 01-APR-03 1AUN 1 JRNL REVDAT 1 04-MAR-98 1AUN 0 JRNL AUTH H.KOIWA,H.KATO,T.NAKATSU,J.ODA,Y.YAMADA,F.SATO JRNL TITL CRYSTAL STRUCTURE OF TOBACCO PR-5D PROTEIN AT 1.8 A JRNL TITL 2 RESOLUTION REVEALS A CONSERVED ACIDIC CLEFT STRUCTURE IN JRNL TITL 3 ANTIFUNGAL THAUMATIN-LIKE PROTEINS. JRNL REF J.MOL.BIOL. V. 286 1137 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10047487 JRNL DOI 10.1006/JMBI.1998.2540 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.KOIWA,H.KATO,T.NAKATSU,J.ODA,Y.YAMADA,F.SATO REMARK 1 TITL PURIFICATION AND CHARACTERIZATION OF TOBACCO REMARK 1 TITL 2 PATHOGENESIS-RELATED PROTEIN PR-5D, AN ANTIFUNGAL REMARK 1 TITL 3 THAUMATIN-LIKE PROTEIN REMARK 1 REF PLANT CELL.PHYSIOL. V. 38 783 1997 REMARK 1 REFN ISSN 0032-0781 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.1 REMARK 3 NUMBER OF REFLECTIONS : 17471 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 SET) : 0.169 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 841 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2206 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 112 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1596 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.170 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.610 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.530 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.750 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.180 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21635 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.3 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 31.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1THV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 0.7 M REMARK 280 MGCL2, 10% GLYCEROL, 50 MM HEPES, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.07000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.07000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.84500 REMARK 290 SMTRY3 4 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 67 69.40 -108.85 REMARK 500 ASN A 106 -42.50 -130.44 REMARK 500 ASP A 185 41.37 -92.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AUN A 1 208 UNP P25871 OLPA_TOBAC 22 229 SEQRES 1 A 208 SER GLY VAL PHE GLU VAL HIS ASN ASN CYS PRO TYR THR SEQRES 2 A 208 VAL TRP ALA ALA ALA THR PRO VAL GLY GLY GLY ARG ARG SEQRES 3 A 208 LEU GLU ARG GLY GLN SER TRP TRP PHE TRP ALA PRO PRO SEQRES 4 A 208 GLY THR LYS MET ALA ARG ILE TRP GLY ARG THR ASN CYS SEQRES 5 A 208 ASN PHE ASP GLY ALA GLY ARG GLY TRP CYS GLN THR GLY SEQRES 6 A 208 ASP CYS GLY GLY VAL LEU GLU CYS LYS GLY TRP GLY LYS SEQRES 7 A 208 PRO PRO ASN THR LEU ALA GLU TYR ALA LEU ASN GLN PHE SEQRES 8 A 208 SER ASN LEU ASP PHE TRP ASP ILE SER VAL ILE ASP GLY SEQRES 9 A 208 PHE ASN ILE PRO MET SER PHE GLY PRO THR LYS PRO GLY SEQRES 10 A 208 PRO GLY LYS CYS HIS GLY ILE GLN CYS THR ALA ASN ILE SEQRES 11 A 208 ASN GLY GLU CYS PRO GLY SER LEU ARG VAL PRO GLY GLY SEQRES 12 A 208 CYS ASN ASN PRO CYS THR THR PHE GLY GLY GLN GLN TYR SEQRES 13 A 208 CYS CYS THR GLN GLY PRO CYS GLY PRO THR GLU LEU SER SEQRES 14 A 208 ARG TRP PHE LYS GLN ARG CYS PRO ASP ALA TYR SER TYR SEQRES 15 A 208 PRO GLN ASP ASP PRO THR SER THR PHE THR CYS THR SER SEQRES 16 A 208 TRP THR THR ASP TYR LYS VAL MET PHE CYS PRO TYR GLY FORMUL 2 HOH *89(H2 O) HELIX 1 1 PHE A 91 ASN A 93 5 3 HELIX 2 2 ILE A 130 GLU A 133 1 4 HELIX 3 3 PRO A 147 THR A 150 1 4 HELIX 4 4 GLN A 154 CYS A 157 1 4 HELIX 5 5 GLU A 167 ARG A 175 1 9 SHEET 1 A 5 SER A 32 TRP A 36 0 SHEET 2 A 5 VAL A 3 ASN A 8 -1 N VAL A 6 O TRP A 33 SHEET 3 A 5 TYR A 200 PHE A 204 1 N TYR A 200 O GLU A 5 SHEET 4 A 5 MET A 109 PRO A 113 -1 N GLY A 112 O LYS A 201 SHEET 5 A 5 ILE A 124 CYS A 126 -1 N CYS A 126 O MET A 109 SHEET 1 B 6 GLY A 23 LEU A 27 0 SHEET 2 B 6 VAL A 14 THR A 19 -1 N ALA A 18 O GLY A 23 SHEET 3 B 6 ALA A 44 THR A 50 -1 N ARG A 49 O TRP A 15 SHEET 4 B 6 LEU A 83 ALA A 87 -1 N TYR A 86 O ALA A 44 SHEET 5 B 6 LEU A 94 SER A 100 -1 N SER A 100 O LEU A 83 SHEET 6 B 6 PHE A 191 THR A 194 -1 N CYS A 193 O ASP A 95 SHEET 1 C 2 CYS A 52 PHE A 54 0 SHEET 2 C 2 GLY A 60 CYS A 62 -1 N TRP A 61 O ASN A 53 SSBOND 1 CYS A 10 CYS A 205 1555 1555 2.03 SSBOND 2 CYS A 52 CYS A 62 1555 1555 2.03 SSBOND 3 CYS A 67 CYS A 73 1555 1555 2.02 SSBOND 4 CYS A 121 CYS A 193 1555 1555 2.03 SSBOND 5 CYS A 126 CYS A 176 1555 1555 2.03 SSBOND 6 CYS A 134 CYS A 144 1555 1555 2.04 SSBOND 7 CYS A 148 CYS A 157 1555 1555 2.04 SSBOND 8 CYS A 158 CYS A 163 1555 1555 2.03 CISPEP 1 THR A 19 PRO A 20 0 -0.10 CISPEP 2 PRO A 79 PRO A 80 0 0.00 CRYST1 80.140 63.690 45.610 90.00 107.18 90.00 C 1 2 1 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 0.012478 0.000000 0.003858 0.00000 SCALE2 0.000000 0.015701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022949 0.00000