HEADER ALLERGEN 02-APR-01 1ICX TITLE CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1A FROM TITLE 2 YELLOW LUPINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN LLR18A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LLPR10.1A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LUPINUS LUTEUS; SOURCE 3 ORGANISM_COMMON: YELLOW LUPINE; SOURCE 4 ORGANISM_TAXID: 3873; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A-LLPR10.1A KEYWDS 7-STRANDED BETA SHEET, C-TERMINAL HELIX, ALLERGEN EXPDTA X-RAY DIFFRACTION AUTHOR J.BIESIADKA,G.BUJACZ,M.M.SIKORSKI,M.JASKOLSKI REVDAT 3 09-AUG-23 1ICX 1 REMARK REVDAT 2 24-FEB-09 1ICX 1 VERSN REVDAT 1 10-JUL-02 1ICX 0 JRNL AUTH J.BIESIADKA,G.BUJACZ,M.M.SIKORSKI,M.JASKOLSKI JRNL TITL CRYSTAL STRUCTURES OF TWO HOMOLOGOUS PATHOGENESIS-RELATED JRNL TITL 2 PROTEINS FROM YELLOW LUPINE. JRNL REF J.MOL.BIOL. V. 319 1223 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12079359 JRNL DOI 10.1016/S0022-2836(02)00385-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.BIESIADKA,M.M.SIKORSKI,G.BUJACZ,M.JASKOLSKI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STRUCTURE REMARK 1 TITL 2 DETERMINATION OF LUPINUS LUTEUS PR10 PROTEIN REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 1925 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444999011221 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.M.SIKORSKI,J.BIESIADKA,A.E.KASPERSKA,J.KOPCINSKA, REMARK 1 AUTH 2 B.LOTOCKA,W.GOLINOWSKI,A.B.LEGOCKI REMARK 1 TITL EXPRESSION OF GENES ENCODING PR10 CLASS PATHOGENESIS-RELATED REMARK 1 TITL 2 PROTEINS IS INHIBITED IN YELLOW LUPINE ROOT NODULES REMARK 1 REF PLANT SCI. V. 149 125 1999 REMARK 1 REFN ISSN 0168-9452 REMARK 1 DOI 10.1016/S0168-9452(99)00148-X REMARK 1 REFERENCE 3 REMARK 1 AUTH M.GAJHEDE,P.OSMARK,F.M.POULSEN,H.IPSEN,J.N.LARSEN, REMARK 1 AUTH 2 R.J.JOOST VAN NEERVEN,C.SCHOU,H.LOWENSTEIN,M.D.SPANGFORT REMARK 1 TITL X-RAY AND NMR STRUCTURE OF BET V 1, THE ORIGIN OF BIRCH REMARK 1 TITL 2 POLLEN ALLERGY REMARK 1 REF NAT.STRUCT.BIOL. V. 3 1040 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 9307 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) : 0.196 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 930 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1318 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 172 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1166 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.190 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) : 2.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.300 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.980 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.430 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 51.41 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 RESIDUES ASP 60, GLN 133, LYS 135, PHE 136 REFINED AS ALANINES REMARK 3 BECAUSE OF POOR SIDE-CHAIN ELECTRON DENSITY REMARK 4 REMARK 4 1ICX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : D41A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3750 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9446 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 19.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.460 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.12700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.460 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 1BTV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, SUCROSE REMARK 280 LAUREATE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.48650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.87750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.30850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.87750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.48650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.30850 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 60 CG OD1 OD2 REMARK 470 GLN A 133 CG CD OE1 NE2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 PHE A 136 CG CD1 CD2 CE1 CE2 CZ 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 THR A 23 -86.47 -120.11 REMARK 500 HIS A 59 78.58 -69.81 REMARK 500 ASP A 60 99.14 53.88 REMARK 500 LYS A 135 -78.51 -79.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BTV RELATED DB: PDB REMARK 900 MAJOR POLLEN ALLERGEN BETV 1 REMARK 900 RELATED ID: 1B6F RELATED DB: PDB REMARK 900 BETV 1-A MUTANT REMARK 900 RELATED ID: 1IFV RELATED DB: PDB REMARK 900 PATHOGENESIS-RELATED PROTEIN LLPR10.1B FROM YELLOW LUPINE DBREF 1ICX A 1 155 UNP P52778 L18A_LUPLU 2 156 SEQRES 1 A 155 GLY ILE PHE ALA PHE GLU ASN GLU GLN SER SER THR VAL SEQRES 2 A 155 ALA PRO ALA LYS LEU TYR LYS ALA LEU THR LYS ASP SER SEQRES 3 A 155 ASP GLU ILE VAL PRO LYS VAL ILE GLU PRO ILE GLN SER SEQRES 4 A 155 VAL GLU ILE VAL GLU GLY ASN GLY GLY PRO GLY THR ILE SEQRES 5 A 155 LYS LYS ILE ILE ALA ILE HIS ASP GLY HIS THR SER PHE SEQRES 6 A 155 VAL LEU HIS LYS LEU ASP ALA ILE ASP GLU ALA ASN LEU SEQRES 7 A 155 THR TYR ASN TYR SER ILE ILE GLY GLY GLU GLY LEU ASP SEQRES 8 A 155 GLU SER LEU GLU LYS ILE SER TYR GLU SER LYS ILE LEU SEQRES 9 A 155 PRO GLY PRO ASP GLY GLY SER ILE GLY LYS ILE ASN VAL SEQRES 10 A 155 LYS PHE HIS THR LYS GLY ASP VAL LEU SER GLU THR VAL SEQRES 11 A 155 ARG ASP GLN ALA LYS PHE LYS GLY LEU GLY LEU PHE LYS SEQRES 12 A 155 ALA ILE GLU GLY TYR VAL LEU ALA HIS PRO ASP TYR FORMUL 2 HOH *104(H2 O) HELIX 1 1 ALA A 14 THR A 23 1 10 HELIX 2 2 ASP A 25 ILE A 34 1 10 HELIX 3 3 GLU A 75 ASN A 77 5 3 HELIX 4 4 PRO A 107 GLY A 109 5 3 HELIX 5 5 SER A 127 ASP A 132 1 6 HELIX 6 6 GLN A 133 HIS A 152 1 20 SHEET 1 A 7 ILE A 2 SER A 11 0 SHEET 2 A 7 SER A 111 THR A 121 -1 N SER A 111 O SER A 11 SHEET 3 A 7 LEU A 94 PRO A 105 -1 N GLU A 95 O HIS A 120 SHEET 4 A 7 THR A 79 GLY A 87 -1 O TYR A 80 N SER A 101 SHEET 5 A 7 THR A 63 ASP A 74 -1 O LEU A 67 N ILE A 85 SHEET 6 A 7 ILE A 52 ILE A 58 -1 N LYS A 53 O HIS A 68 SHEET 7 A 7 ILE A 37 GLU A 44 -1 N GLN A 38 O ILE A 56 CRYST1 34.973 56.617 61.755 90.00 90.00 90.00 P 21 21 21 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 0.028593 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016193 0.00000