10 20 30 40 50 60 70 80 2I0W - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIFUNGAL PROTEIN 11-AUG-06 2I0W
TITLE CRYSTAL STRUCTURE ANALYSIS OF NP24-I, A THAUMATIN-LIKE TITLE 2 PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NP24; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PATHOGENESIS-RELATED PROTEIN PR P23, SALT-INDUCED COMPND 5 PROTEIN
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 3 ORGANISM_TAXID: 4081; SOURCE 4 OTHER_DETAILS: RIPE TOMATO
KEYWDS ALPHA-BETA PROTEIN, ANTIFUNGAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR C.CHAKRABARTI,R.GHOSH
REVDAT 4 24-FEB-09 2I0W 1 VERSN REVDAT 3 16-SEP-08 2I0W 1 JRNL REVDAT 2 09-SEP-08 2I0W 1 JRNL REVDAT 1 24-JUL-07 2I0W 0
JRNL AUTH R.GHOSH,C.CHAKRABARTI JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF NP24-I: A JRNL TITL 2 THAUMATIN-LIKE PROTEIN JRNL REF PLANTA V. 228 883 2008 JRNL REFN ISSN 0032-0935 JRNL PMID 18651170 JRNL DOI 10.1007/S00425-008-0790-5
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 988975.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 8035 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) : 0.171 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 415 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 841 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1553 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.93000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.85 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) : 3.730 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.750 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.500 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.480; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 36.15 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2I0W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB038997.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 6.7 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MULTILAYER REMARK 200 OPTICS : OSMIC MULTILAYERS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : AUTOMAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8574 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.060 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.04 REMARK 200 R MERGE FOR SHELL (I) : 0.33690 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PCV REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M LITHIUM CHLORIDE, 20% PEG REMARK 280 3350, PH 6.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K
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 31.44750 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 47.17125 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 15.72375 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 ALA A 55 -37.49 -34.02 REMARK 500 CYS A 66 52.80 -113.86 REMARK 500 ASN A 105 -39.51 -145.29 REMARK 500 CYS A 125 79.00 -155.00 REMARK 500 ASP A 184 39.68 -89.96 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 CL A 208
DBREF 2I0W A 1 207 UNP P12670 NP24_LYCES 22 228
SEQRES 1 A 207 ALA THR ILE GLU VAL ARG ASN ASN CYS PRO TYR THR VAL SEQRES 2 A 207 TRP ALA ALA SER THR PRO ILE GLY GLY GLY ARG ARG LEU SEQRES 3 A 207 ASN ARG GLY GLN THR TRP VAL ILE ASN ALA PRO ARG GLY SEQRES 4 A 207 THR LYS MET ALA ARG ILE TRP GLY ARG THR GLY CYS ASN SEQRES 5 A 207 PHE ASN ALA ALA GLY ARG GLY THR CYS GLN THR GLY ASP SEQRES 6 A 207 CYS GLY GLY VAL LEU GLN CYS THR GLY TRP GLY LYS PRO SEQRES 7 A 207 PRO ASN THR LEU ALA GLU TYR ALA LEU ASP GLN PHE SER SEQRES 8 A 207 ASN LEU ASP PHE TRP ASP ILE SER LEU VAL ASP GLY PHE SEQRES 9 A 207 ASN ILE PRO MET THR PHE ALA PRO THR LYS PRO SER GLY SEQRES 10 A 207 GLY LYS CYS HIS ALA ILE HIS CYS THR ALA ASN ILE ASN SEQRES 11 A 207 GLY GLU CYS PRO ARG ALA LEU LYS VAL PRO GLY GLY CYS SEQRES 12 A 207 ASN ASN PRO CYS THR THR PHE GLY GLY GLN GLN TYR CYS SEQRES 13 A 207 CYS THR GLN GLY PRO CYS GLY PRO THR GLU LEU SER LYS SEQRES 14 A 207 PHE PHE LYS LYS ARG CYS PRO ASP ALA TYR SER TYR PRO SEQRES 15 A 207 GLN ASP ASP PRO THR SER THR PHE THR CYS PRO GLY GLY SEQRES 16 A 207 SER THR ASN TYR ARG VAL VAL PHE CYS PRO ASN GLY
HET CL A 208 1
HETNAM CL CHLORIDE ION
FORMUL 2 CL CL 1- FORMUL 3 HOH *67(H2 O)
HELIX 1 1 ASN A 128 CYS A 133 1 6 HELIX 2 2 ASN A 145 PHE A 150 1 6 HELIX 3 3 GLY A 152 CYS A 157 1 6 HELIX 4 4 LEU A 167 CYS A 175 1 9
SHEET 1 A 5 THR A 31 ASN A 35 0 SHEET 2 A 5 THR A 2 ASN A 7 -1 N VAL A 5 O TRP A 32 SHEET 3 A 5 TYR A 199 PHE A 203 1 O VAL A 201 N GLU A 4 SHEET 4 A 5 MET A 108 PRO A 112 -1 N ALA A 111 O ARG A 200 SHEET 5 A 5 ILE A 123 CYS A 125 -1 O ILE A 123 N PHE A 110 SHEET 1 B 6 GLY A 22 LEU A 26 0 SHEET 2 B 6 VAL A 13 THR A 18 -1 N VAL A 13 O LEU A 26 SHEET 3 B 6 ALA A 43 ARG A 48 -1 O TRP A 46 N ALA A 16 SHEET 4 B 6 LEU A 82 ASP A 88 -1 O ALA A 83 N ILE A 45 SHEET 5 B 6 LEU A 93 SER A 99 -1 O PHE A 95 N ALA A 86 SHEET 6 B 6 PHE A 190 PRO A 193 -1 O CYS A 192 N ASP A 94 SHEET 1 C 2 ASN A 52 ASN A 54 0 SHEET 2 C 2 ARG A 58 THR A 60 -1 O ARG A 58 N ASN A 54 SHEET 1 D 2 LYS A 138 VAL A 139 0 SHEET 2 D 2 GLY A 142 CYS A 143 -1 O GLY A 142 N VAL A 139
SSBOND 1 CYS A 9 CYS A 204 1555 1555 2.02 SSBOND 2 CYS A 51 CYS A 61 1555 1555 2.03 SSBOND 3 CYS A 66 CYS A 72 1555 1555 2.03 SSBOND 4 CYS A 120 CYS A 192 1555 1555 2.03 SSBOND 5 CYS A 125 CYS A 175 1555 1555 2.05 SSBOND 6 CYS A 133 CYS A 143 1555 1555 2.04 SSBOND 7 CYS A 147 CYS A 156 1555 1555 2.03 SSBOND 8 CYS A 157 CYS A 162 1555 1555 2.02
CISPEP 1 THR A 18 PRO A 19 0 0.33 CISPEP 2 PRO A 78 PRO A 79 0 0.67
SITE 1 AC1 4 ASN A 35 PRO A 37 ARG A 200 HOH A 247
CRYST1 61.010 61.010 62.895 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 0.016391 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016391 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015900 0.00000