HEADER ALLERGEN 16-FEB-18 6FRR TITLE STRUCTURAL AND IMMUNOLOGICAL PROPERTIES OF THE ALLERGEN ART V 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SPECIFIC LIPID-TRANSFER PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTEMISIA VULGARIS; SOURCE 3 ORGANISM_COMMON: MUGWORT; SOURCE 4 ORGANISM_TAXID: 4220; SOURCE 5 GENE: ART V 3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA GAMI2 PLYSS KEYWDS ART V 3.0201 LIPID BINDING PROTEIN, ALLERGEN EXPDTA X-RAY DIFFRACTION AUTHOR H.BRANDSTETTER,W.T.SOH,I.MAGLER REVDAT 3 17-JAN-24 6FRR 1 REMARK REVDAT 2 25-MAR-20 6FRR 1 JRNL REVDAT 1 13-MAR-19 6FRR 0 JRNL AUTH S.WILDNER,I.GRIESSNER,T.STEMESEDER,C.REGL,W.T.SOH,L.G.STOCK, JRNL AUTH 2 T.VOLKER,C.ALESSANDRI,A.MARI,C.G.HUBER,H.STUTZ, JRNL AUTH 3 H.BRANDSTETTER,G.GADERMAIER JRNL TITL BOILING DOWN THE CYSTEINE-STABILIZED LTP FOLD - LOSS OF JRNL TITL 2 STRUCTURAL AND IMMUNOLOGICAL INTEGRITY OF ALLERGENIC ART V 3 JRNL TITL 3 AND PRU P 3 AS A CONSEQUENCE OF IRREVERSIBLE LANTHIONINE JRNL TITL 4 FORMATION. JRNL REF MOL.IMMUNOL. V. 116 140 2019 JRNL REFN ISSN 0161-5890 JRNL PMID 31654938 JRNL DOI 10.1016/J.MOLIMM.2019.10.012 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14560 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 733 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.4177 - 3.3299 0.99 2906 136 0.1842 0.2269 REMARK 3 2 3.3299 - 2.6431 0.99 2796 129 0.2088 0.2753 REMARK 3 3 2.6431 - 2.3090 1.00 2735 145 0.1896 0.2369 REMARK 3 4 2.3090 - 2.0979 0.99 2697 153 0.1838 0.2552 REMARK 3 5 2.0979 - 1.9476 1.00 2693 170 0.2087 0.2934 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.70 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1419 REMARK 3 ANGLE : 0.828 1916 REMARK 3 CHIRALITY : 0.050 220 REMARK 3 PLANARITY : 0.005 242 REMARK 3 DIHEDRAL : 13.837 910 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.948 REMARK 200 RESOLUTION RANGE LOW (A) : 52.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 2ALG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M AMMONIUM SULPHATE, 0.1 M HEPES, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.97333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.48667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.48667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.97333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 64 CB OG REMARK 480 LYS A 92 CD CE NZ REMARK 480 LYS B 3 CE NZ REMARK 480 LYS B 53 CD CE NZ 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 GLN B 20 42.78 -142.76 REMARK 500 PRO B 79 23.38 -79.47 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 A 311 DISTANCE = 7.56 ANGSTROMS REMARK 525 HOH A 312 DISTANCE = 8.29 ANGSTROMS REMARK 525 HOH B 279 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH B 280 DISTANCE = 9.81 ANGSTROMS REMARK 525 HOH B 281 DISTANCE = 10.02 ANGSTROMS REMARK 525 HOH B 282 DISTANCE = 15.94 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 DBREF 6FRR A 3 92 UNP C4MGG9 C4MGG9_ARTVU 25 114 DBREF 6FRR B 3 92 UNP C4MGG9 C4MGG9_ARTVU 25 114 SEQADV 6FRR MET A 1 UNP C4MGG9 INITIATING METHIONINE SEQADV 6FRR ILE A 2 UNP C4MGG9 EXPRESSION TAG SEQADV 6FRR MET B 1 UNP C4MGG9 INITIATING METHIONINE SEQADV 6FRR ILE B 2 UNP C4MGG9 EXPRESSION TAG SEQRES 1 A 92 MET ILE LYS CYS SER ASP VAL SER ASN LYS ILE SER ALA SEQRES 2 A 92 CYS LEU SER TYR LEU LYS GLN GLY GLY GLU VAL PRO ALA SEQRES 3 A 92 ASP CYS CYS THR GLY VAL LYS GLY LEU ASN ASP ALA ALA SEQRES 4 A 92 LYS THR THR PRO ASP ARG GLN THR ALA CYS ASN CYS LEU SEQRES 5 A 92 LYS THR THR PHE LYS SER ASN LYS ASP PHE LYS SER ASP SEQRES 6 A 92 PHE ALA ALA SER LEU PRO SER LYS CYS GLY VAL ASN ILE SEQRES 7 A 92 PRO TYR LYS ILE SER LEU GLU THR ASP CYS ASN LYS VAL SEQRES 8 A 92 LYS SEQRES 1 B 92 MET ILE LYS CYS SER ASP VAL SER ASN LYS ILE SER ALA SEQRES 2 B 92 CYS LEU SER TYR LEU LYS GLN GLY GLY GLU VAL PRO ALA SEQRES 3 B 92 ASP CYS CYS THR GLY VAL LYS GLY LEU ASN ASP ALA ALA SEQRES 4 B 92 LYS THR THR PRO ASP ARG GLN THR ALA CYS ASN CYS LEU SEQRES 5 B 92 LYS THR THR PHE LYS SER ASN LYS ASP PHE LYS SER ASP SEQRES 6 B 92 PHE ALA ALA SER LEU PRO SER LYS CYS GLY VAL ASN ILE SEQRES 7 B 92 PRO TYR LYS ILE SER LEU GLU THR ASP CYS ASN LYS VAL SEQRES 8 B 92 LYS HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 B 101 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *194(H2 O) HELIX 1 AA1 LYS A 3 SER A 12 1 10 HELIX 2 AA2 CYS A 14 GLY A 21 1 8 HELIX 3 AA3 PRO A 25 ALA A 39 1 15 HELIX 4 AA4 THR A 41 SER A 58 1 18 HELIX 5 AA5 LYS A 63 GLY A 75 1 13 HELIX 6 AA6 ASP A 87 VAL A 91 5 5 HELIX 7 AA7 LYS B 3 ILE B 11 1 9 HELIX 8 AA8 CYS B 14 GLY B 21 1 8 HELIX 9 AA9 PRO B 25 ALA B 38 1 14 HELIX 10 AB1 THR B 41 ASN B 59 1 19 HELIX 11 AB2 LYS B 63 CYS B 74 1 12 HELIX 12 AB3 ASP B 87 VAL B 91 5 5 SSBOND 1 CYS A 4 CYS A 51 1555 1555 2.05 SSBOND 2 CYS A 14 CYS A 28 1555 1555 2.05 SSBOND 3 CYS A 29 CYS A 74 1555 1555 2.04 SSBOND 4 CYS A 49 CYS A 88 1555 1555 2.05 SSBOND 5 CYS B 4 CYS B 51 1555 1555 2.05 SSBOND 6 CYS B 14 CYS B 28 1555 1555 2.03 SSBOND 7 CYS B 29 CYS B 74 1555 1555 2.03 SSBOND 8 CYS B 49 CYS B 88 1555 1555 2.04 SITE 1 AC1 5 SER A 12 ASN A 59 HOH A 206 HOH A 210 SITE 2 AC1 5 HOH A 238 SITE 1 AC2 3 ARG A 45 HOH A 262 LYS B 33 SITE 1 AC3 6 LYS A 60 LYS B 3 CYS B 4 SER B 5 SITE 2 AC3 6 HOH B 219 HOH B 254 CRYST1 60.398 60.398 91.460 90.00 90.00 120.00 P 32 2 1 12 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 0.016557 0.009559 0.000000 0.00000 SCALE2 0.000000 0.019118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010934 0.00000