HEADER ALLERGEN 23-JAN-19 6NRE TITLE MONOMERIC LIPOCALIN CAN F 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOCALIN-CAN F 6 ALLERGEN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 3 ORGANISM_COMMON: DOG; SOURCE 4 ORGANISM_TAXID: 9615; SOURCE 5 GENE: LCN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPOCALIN, METABOLIC ROLE, ALLERGEN EXPDTA X-RAY DIFFRACTION AUTHOR M.CLAYTON G,W.KAPPLER J,S.CHAN REVDAT 2 06-NOV-24 6NRE 1 REMARK REVDAT 1 25-SEP-19 6NRE 0 JRNL AUTH G.M.CLAYTON,J.WHITE,S.LEE,J.W.KAPPLER,S.K.CHAN JRNL TITL STRUCTURAL CHARACTERISTICS OF LIPOCALIN ALLERGENS: CRYSTAL JRNL TITL 2 STRUCTURE OF THE IMMUNOGENIC DOG ALLERGEN CAN F 6. JRNL REF PLOS ONE V. 14 13052 2019 JRNL REFN ESSN 1932-6203 JRNL PMID 31525203 JRNL DOI 10.1371/JOURNAL.PONE.0213052 REMARK 2 REMARK 2 RESOLUTION. 2.06 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 22536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 1063 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 58.1800 - 4.1130 1.00 2727 117 0.1879 0.2084 REMARK 3 2 4.1130 - 3.2647 1.00 2714 133 0.2076 0.2194 REMARK 3 3 3.2647 - 2.8520 1.00 2694 150 0.2526 0.2779 REMARK 3 4 2.8520 - 2.5912 1.00 2687 110 0.2714 0.3763 REMARK 3 5 2.5912 - 2.4055 1.00 2711 140 0.2843 0.3505 REMARK 3 6 2.4055 - 2.2637 1.00 2687 168 0.2791 0.2922 REMARK 3 7 2.2637 - 2.1503 0.99 2709 102 0.2913 0.3024 REMARK 3 8 2.1503 - 2.0567 0.94 2544 143 0.3345 0.3954 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.004 1275 REMARK 3 ANGLE : 0.672 1723 REMARK 3 CHIRALITY : 0.051 198 REMARK 3 PLANARITY : 0.003 219 REMARK 3 DIHEDRAL : 15.795 773 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 6NRE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239270. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12122 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 72.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL, SODIUM ACETATE, REMARK 280 POLYETHYLENE GLYCOL ETHER 550, PH 4.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 24.16267 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 48.32533 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 48.32533 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 24.16267 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: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 ASN A 5 REMARK 465 SER A 166 REMARK 465 GLU A 167 REMARK 465 ALA A 168 REMARK 465 ALA A 169 REMARK 465 GLN A 170 REMARK 465 VAL A 171 REMARK 465 SER A 172 REMARK 465 SER A 173 REMARK 465 ALA A 174 REMARK 465 GLU A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 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 6 CG OD1 OD2 REMARK 470 ASN A 11 CG OD1 ND2 REMARK 470 GLU A 35 CG CD OE1 OE2 REMARK 470 GLU A 48 CG CD OE1 OE2 REMARK 470 ASN A 52 CG OD1 ND2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 ASP A 88 CG OD1 OD2 REMARK 470 GLU A 101 CG CD OE1 OE2 REMARK 470 GLN A 113 CG CD OE1 NE2 REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 GLU A 135 CG CD OE1 OE2 REMARK 470 GLN A 165 CG CD OE1 NE2 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 37 1.70 86.56 REMARK 500 PRO A 127 5.17 -60.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 6NRE A 1 175 UNP H2B3G5 H2B3G5_CANLF 16 190 SEQADV 6NRE HIS A 176 UNP H2B3G5 EXPRESSION TAG SEQADV 6NRE HIS A 177 UNP H2B3G5 EXPRESSION TAG SEQADV 6NRE HIS A 178 UNP H2B3G5 EXPRESSION TAG SEQADV 6NRE HIS A 179 UNP H2B3G5 EXPRESSION TAG SEQADV 6NRE HIS A 180 UNP H2B3G5 EXPRESSION TAG SEQADV 6NRE HIS A 181 UNP H2B3G5 EXPRESSION TAG SEQRES 1 A 181 HIS GLU GLU GLU ASN ASP VAL VAL LYS GLY ASN PHE ASP SEQRES 2 A 181 ILE SER LYS ILE SER GLY ASP TRP TYR SER ILE LEU LEU SEQRES 3 A 181 ALA SER ASP ILE LYS GLU LYS ILE GLU GLU ASN GLY SER SEQRES 4 A 181 MET ARG VAL PHE VAL LYS ASP ILE GLU VAL LEU SER ASN SEQRES 5 A 181 SER SER LEU ILE PHE THR MET HIS THR LYS VAL ASN GLY SEQRES 6 A 181 LYS CYS THR LYS ILE SER LEU ILE CYS ASN LYS THR GLU SEQRES 7 A 181 LYS ASP GLY GLU TYR ASP VAL VAL HIS ASP GLY TYR ASN SEQRES 8 A 181 LEU PHE ARG ILE ILE GLU THR ALA TYR GLU ASP TYR ILE SEQRES 9 A 181 ILE PHE HIS LEU ASN ASN VAL ASN GLN GLU GLN GLU PHE SEQRES 10 A 181 GLN LEU MET GLU LEU TYR GLY ARG LYS PRO ASP VAL SER SEQRES 11 A 181 PRO LYS VAL LYS GLU LYS PHE VAL ARG TYR CYS GLN GLY SEQRES 12 A 181 MET GLU ILE PRO LYS GLU ASN ILE LEU ASP LEU THR GLN SEQRES 13 A 181 VAL ASP ARG CYS LEU GLN ALA ARG GLN SER GLU ALA ALA SEQRES 14 A 181 GLN VAL SER SER ALA GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *13(H2 O) HELIX 1 AA1 ASP A 13 SER A 18 5 6 HELIX 2 AA2 ILE A 30 ILE A 34 5 5 HELIX 3 AA3 SER A 130 MET A 144 1 15 HELIX 4 AA4 PRO A 147 GLU A 149 5 3 HELIX 5 AA5 CYS A 160 ARG A 164 5 5 SHEET 1 AA110 GLY A 19 ASP A 20 0 SHEET 2 AA110 PHE A 43 VAL A 49 -1 O ILE A 47 N GLY A 19 SHEET 3 AA110 SER A 54 VAL A 63 -1 O THR A 58 N LYS A 45 SHEET 4 AA110 LYS A 66 LYS A 76 -1 O CYS A 74 N LEU A 55 SHEET 5 AA110 GLU A 82 VAL A 86 -1 O ASP A 84 N ASN A 75 SHEET 6 AA110 TYR A 90 ALA A 99 -1 O ASN A 91 N VAL A 85 SHEET 7 AA110 TYR A 103 VAL A 111 -1 O ASN A 109 N LEU A 92 SHEET 8 AA110 PHE A 117 GLY A 124 -1 O LEU A 119 N LEU A 108 SHEET 9 AA110 TYR A 22 SER A 28 -1 N ALA A 27 O MET A 120 SHEET 10 AA110 ILE A 151 ASP A 153 -1 O LEU A 152 N LEU A 26 SSBOND 1 CYS A 67 CYS A 160 1555 1555 2.03 CRYST1 67.154 67.154 72.488 90.00 90.00 120.00 P 31 2 1 6 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 0.014891 0.008597 0.000000 0.00000 SCALE2 0.000000 0.017195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013795 0.00000