HEADER ALLERGEN 28-FEB-02 1L3P TITLE CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE MAJOR GRASS POLLEN TITLE 2 ALLERGEN PHL P 5B COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLLEN ALLERGEN PHL P 5B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHL P VB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHLEUM PRATENSE; SOURCE 3 ORGANISM_COMMON: TIMOTHY GRASS; SOURCE 4 ORGANISM_TAXID: 15957; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMALC KEYWDS GRASS POLLEN ALLERGEN, PHL P 5B, ALLERGY, ALLERGEN EXPDTA X-RAY DIFFRACTION AUTHOR K.R.RAJASHANKAR,A.BUFE,W.WEBER,S.ESCHENBURG,B.LINDNER,C.BETZEL REVDAT 8 20-NOV-24 1L3P 1 REMARK REVDAT 7 03-APR-24 1L3P 1 REMARK LINK REVDAT 6 11-OCT-17 1L3P 1 REMARK REVDAT 5 08-FEB-17 1L3P 1 JRNL REVDAT 4 01-FEB-17 1L3P 1 AUTHOR REVDAT 3 13-JUL-11 1L3P 1 VERSN REVDAT 2 24-FEB-09 1L3P 1 VERSN REVDAT 1 28-FEB-03 1L3P 0 JRNL AUTH K.RAJASHANKAR,A.BUFE,W.WEBER,S.ESCHENBURG,B.LINDNER,C.BETZEL JRNL TITL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE MAJOR GRASS-POLLEN JRNL TITL 2 ALLERGEN PHLP 5B. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 1175 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 12077438 JRNL DOI 10.1107/S0907444902007254 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.BUFE,C.BETZEL,G.SCHRAMM,A.PETERSEN,W.M.BECKER,M.SCHLAAK, REMARK 1 AUTH 2 M.PERBANDT,Z.DAUTER,W.WEBER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY DIFFRACTION DATA OF A MAJOR REMARK 1 TITL 2 POLLEN ALLERGEN. CRYSTAL GROWTH SEPARATES A LOW MOLECULAR REMARK 1 TITL 3 WEIGHT FORM WITH ELEVATED BIOLOGICAL ACTIVITY REMARK 1 REF J.BIOL.CHEM. V. 271 27193 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.271.44.27193 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 7037 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) : 0.193 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 350 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.30 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L3P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7037 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 7.380 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.23 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: HG DERIVATIVE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M PHOSPHATE, 0.5MM MGCL2, PH 4.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 53.90200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.90200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.48750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.17750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.48750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.17750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.90200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.48750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.17750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.90200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.48750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.17750 REMARK 290 SMTRY3 8 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 300 REMARK: THE SECOND PART OF THE DIMER IS GENERATED BY THE SYMMETRY REMARK 300 OPERATION X,-Y,-Z 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 38.97500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.90200 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 255 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 303 LIES ON A SPECIAL POSITION. 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 GLN A 156 CD OE1 NE2 REMARK 470 GLN A 215 CD OE1 NE2 REMARK 470 GLN A 251 CD OE1 NE2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 350 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 170 OG1 REMARK 620 2 HOH A 253 O 86.2 REMARK 620 3 HOH A 263 O 123.0 124.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 350 REMARK 999 REMARK 999 SEQUENCE AUTHOR STATES THAT RESIDUE 195 IS SERINE, BUT BOTH REMARK 999 SERINE AND THREONINE ARE IN DUAL CONFORMATION. DBREF 1L3P A 150 251 UNP Q40963 MPA5B_PHLPR 150 251 SEQADV 1L3P THR A 195 UNP Q40963 SER 195 SEE REMARK 999 SEQRES 1 A 102 ILE PRO ALA GLY GLU LEU GLN ILE ILE ASP LYS ILE ASP SEQRES 2 A 102 ALA ALA PHE LYS VAL ALA ALA THR ALA ALA ALA THR ALA SEQRES 3 A 102 PRO ALA ASP ASP LYS PHE THR VAL PHE GLU ALA ALA PHE SEQRES 4 A 102 ASN LYS ALA ILE LYS GLU THR THR GLY GLY ALA TYR ASP SEQRES 5 A 102 THR TYR LYS CYS ILE PRO SER LEU GLU ALA ALA VAL LYS SEQRES 6 A 102 GLN ALA TYR ALA ALA THR VAL ALA ALA ALA PRO GLN VAL SEQRES 7 A 102 LYS TYR ALA VAL PHE GLU ALA ALA LEU THR LYS ALA ILE SEQRES 8 A 102 THR ALA MET SER GLU VAL GLN LYS VAL SER GLN HET PO4 A 252 5 HET MG A 350 1 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION FORMUL 2 PO4 O4 P 3- FORMUL 3 MG MG 2+ FORMUL 4 HOH *97(H2 O) HELIX 1 1 PRO A 151 GLN A 156 1 6 HELIX 2 2 ILE A 157 THR A 174 1 18 HELIX 3 3 ALA A 175 ALA A 175 5 1 HELIX 4 4 PRO A 176 ASP A 178 5 3 HELIX 5 5 ASP A 179 THR A 196 1 18 HELIX 6 6 THR A 202 CYS A 205 5 4 HELIX 7 7 ILE A 206 ALA A 219 1 14 HELIX 8 8 ALA A 224 GLN A 226 5 3 HELIX 9 9 VAL A 227 GLN A 251 1 25 SSBOND 1 CYS A 205 CYS A 205 1555 4566 2.44 LINK OG1 THR A 170 MG MG A 350 1555 1555 2.77 LINK O HOH A 253 MG MG A 350 1555 1555 2.84 LINK O HOH A 263 MG MG A 350 3655 1555 2.81 SITE 1 AC1 9 ALA A 173 ALA A 177 LYS A 180 GLN A 226 SITE 2 AC1 9 GLU A 233 HOH A 253 HOH A 254 HOH A 256 SITE 3 AC1 9 HOH A 306 SITE 1 AC2 4 THR A 170 ALA A 177 HOH A 253 HOH A 263 CRYST1 38.975 50.355 107.804 90.00 90.00 90.00 C 2 2 21 8 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 0.025657 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019859 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009276 0.00000