HEADER ALLERGEN 25-OCT-99 1QNX TITLE VES V 5, AN ALLERGEN FROM VESPULA VULGARIS VENOM COMPND MOL_ID: 1; COMPND 2 MOLECULE: VES V 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTIGEN 5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VESPULA VULGARIS; SOURCE 3 ORGANISM_COMMON: YELLOW JACKET; SOURCE 4 ORGANISM_TAXID: 7454; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTIGEN 5, ALLERGEN, VESPID VENOM EXPDTA X-RAY DIFFRACTION AUTHOR A.HENRIKSEN,M.GAJHEDE,M.D.SPANGFORT REVDAT 4 17-JAN-18 1QNX 1 REMARK REVDAT 3 24-FEB-09 1QNX 1 VERSN REVDAT 2 04-DEC-01 1QNX 1 JRNL REVDAT 1 26-OCT-00 1QNX 0 JRNL AUTH A.HENRIKSEN,T.P.KING,O.MIRZA,R.I.MONSALVE,K.MENO,H.IPSEN, JRNL AUTH 2 J.N.LARSEN,M.GAJHEDE,M.D.SPANGFORT JRNL TITL MAJOR VENOM ALLERGEN OF YELLOW JACKETS, VES V 5: STRUCTURAL JRNL TITL 2 CHARACTERIZATION OF A PATHOGENESIS-RELATED PROTEIN JRNL TITL 3 SUPERFAMILY. JRNL REF PROTEINS: STRUCT.,FUNCT., V. 45 438 2001 JRNL REF 2 GENET. JRNL REFN ISSN 0887-3585 JRNL PMID 11746691 JRNL DOI 10.1002/PROT.1160 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 799294.980 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 17556 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) : 0.209 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 845 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2863 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 136 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1676 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.06000 REMARK 3 B22 (A**2) : 4.19000 REMARK 3 B33 (A**2) : -0.13000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.03 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 0.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.850 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.780 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.500 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 36.90 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 1QNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1290004313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.959 REMARK 200 MONOCHROMATOR : NULL 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 : 17809 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.17800 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: CNS 0.5, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG6000, 0.1M CITRTE BUFFER PH REMARK 280 5.6, PH 5.60 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 22.67950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.38850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.08950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.38850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.67950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.08950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 ASN A 92 0.09 -66.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2010 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH A2020 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A2021 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A2057 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2062 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH A2063 DISTANCE = 7.17 ANGSTROMS 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 NA A 458 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 42 OE1 REMARK 620 2 HOH A2092 O 89.3 REMARK 620 3 GLY A 63 O 172.2 91.5 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 NA A 458 DBREF 1QNX A -4 0 PDB 1QNX 1QNX -4 0 DBREF 1QNX A 1 204 UNP Q05110 VA5_VESVU 24 227 SEQADV 1QNX LYS A 196 UNP Q05110 MET 219 CONFLICT SEQRES 1 A 209 ALA GLU ALA GLU PHE ASN ASN TYR CYS LYS ILE LYS CYS SEQRES 2 A 209 LEU LYS GLY GLY VAL HIS THR ALA CYS LYS TYR GLY SER SEQRES 3 A 209 LEU LYS PRO ASN CYS GLY ASN LYS VAL VAL VAL SER TYR SEQRES 4 A 209 GLY LEU THR LYS GLN GLU LYS GLN ASP ILE LEU LYS GLU SEQRES 5 A 209 HIS ASN ASP PHE ARG GLN LYS ILE ALA ARG GLY LEU GLU SEQRES 6 A 209 THR ARG GLY ASN PRO GLY PRO GLN PRO PRO ALA LYS ASN SEQRES 7 A 209 MET LYS ASN LEU VAL TRP ASN ASP GLU LEU ALA TYR VAL SEQRES 8 A 209 ALA GLN VAL TRP ALA ASN GLN CYS GLN TYR GLY HIS ASP SEQRES 9 A 209 THR CYS ARG ASP VAL ALA LYS TYR GLN VAL GLY GLN ASN SEQRES 10 A 209 VAL ALA LEU THR GLY SER THR ALA ALA LYS TYR ASP ASP SEQRES 11 A 209 PRO VAL LYS LEU VAL LYS MET TRP GLU ASP GLU VAL LYS SEQRES 12 A 209 ASP TYR ASN PRO LYS LYS LYS PHE SER GLY ASN ASP PHE SEQRES 13 A 209 LEU LYS THR GLY HIS TYR THR GLN MET VAL TRP ALA ASN SEQRES 14 A 209 THR LYS GLU VAL GLY CYS GLY SER ILE LYS TYR ILE GLN SEQRES 15 A 209 GLU LYS TRP HIS LYS HIS TYR LEU VAL CYS ASN TYR GLY SEQRES 16 A 209 PRO SER GLY ASN PHE LYS ASN GLU GLU LEU TYR GLN THR SEQRES 17 A 209 LYS HET NA A 458 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *251(H2 O) HELIX 1 1 ALA A -4 ASN A 1 5 6 HELIX 2 2 ASN A 2 ILE A 6 5 5 HELIX 3 3 HIS A 14 TYR A 19 1 6 HELIX 4 4 THR A 37 ARG A 57 1 21 HELIX 5 5 ASN A 80 ASN A 92 1 13 HELIX 6 6 ASP A 125 ASP A 135 1 11 HELIX 7 7 GLU A 136 TYR A 140 5 5 HELIX 8 8 LYS A 145 ASN A 149 5 5 HELIX 9 9 ASP A 150 GLY A 155 1 6 HELIX 10 10 THR A 154 VAL A 161 1 8 SHEET 1 A 4 GLY A 110 SER A 118 0 SHEET 2 A 4 TRP A 180 GLY A 190 -1 N TYR A 189 O GLY A 110 SHEET 3 A 4 GLU A 167 GLN A 177 -1 N GLN A 177 O TRP A 180 SHEET 4 A 4 VAL A 30 TYR A 34 -1 N SER A 33 O LYS A 174 SSBOND 1 CYS A 4 CYS A 17 1555 1555 2.04 SSBOND 2 CYS A 8 CYS A 101 1555 1555 2.02 SSBOND 3 CYS A 26 CYS A 94 1555 1555 2.02 SSBOND 4 CYS A 170 CYS A 187 1555 1555 2.05 LINK NA NA A 458 OE1 GLN A 42 1555 3545 2.51 LINK NA NA A 458 O HOH A2092 1555 3545 2.60 LINK NA NA A 458 O GLY A 63 1555 1555 2.50 CISPEP 1 ASN A 64 PRO A 65 0 0.31 CISPEP 2 GLY A 66 PRO A 67 0 0.25 CISPEP 3 GLY A 190 PRO A 191 0 -0.66 SITE 1 AC1 6 GLN A 42 GLY A 63 HOH A2092 HOH A2129 SITE 2 AC1 6 HOH A2135 HOH A2203 CRYST1 45.359 62.179 82.777 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 0.022046 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012081 0.00000