HEADER TRANSPORT PROTEIN 13-JUL-22 8AEJ TITLE X-RAY STRUCTURE OF CANIS FAMILIARIS ODORANT BINDING PROTEIN 3 BOUND TO TITLE 2 MENTHONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOCALIN CAN F 6.0101; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALLERGEN CAN F 6; COMPND 5 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ODORANT BINDING PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHWARTZ,L.BRIAND REVDAT 1 16-AUG-23 8AEJ 0 JRNL AUTH M.GLAZ,M.SCHWARTZ,L.BRIAND JRNL TITL STRUCTURE OF DOG ODORANT BINDING PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16661 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.290 REMARK 3 FREE R VALUE TEST SET COUNT : 881 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 45.2100 - 3.3400 1.00 2765 144 0.1839 0.2051 REMARK 3 2 3.3400 - 2.6500 1.00 2644 144 0.2367 0.2776 REMARK 3 3 2.6500 - 2.3200 1.00 2615 147 0.2659 0.3313 REMARK 3 4 2.3200 - 2.1100 1.00 2611 136 0.2651 0.3388 REMARK 3 5 2.1100 - 1.9600 1.00 2591 140 0.2744 0.3602 REMARK 3 6 1.9600 - 1.8400 0.99 2554 170 0.2851 0.3569 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) : 0.239 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.64 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 : 0.012 1336 REMARK 3 ANGLE : 1.219 1797 REMARK 3 CHIRALITY : 0.073 201 REMARK 3 PLANARITY : 0.007 230 REMARK 3 DIHEDRAL : 21.308 514 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 8AEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124230. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978564 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16710 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 45.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 19.90 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6NRE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 550, 6% 2-PROPANOL IN 0.1 M PH REMARK 280 4.6 SODIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 23.99500 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 47.99000 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 47.99000 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 23.99500 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 MET A -12 REMARK 465 ARG A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 THR A -2 REMARK 465 ASP A -1 REMARK 465 PRO A 0 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 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 -4.19 78.59 REMARK 500 LYS A 45 -62.86 -107.29 REMARK 500 SER A 53 12.13 -146.77 REMARK 500 HIS A 87 117.67 -173.87 REMARK 500 ASP A 102 -56.55 -130.16 REMARK 500 PRO A 127 1.55 -56.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 8AEJ A 1 175 UNP H2B3G5 LI601_CANLF 16 190 SEQADV 8AEJ MET A -12 UNP H2B3G5 INITIATING METHIONINE SEQADV 8AEJ ARG A -11 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ GLY A -10 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ SER A -9 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ HIS A -8 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ HIS A -7 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ HIS A -6 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ HIS A -5 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ HIS A -4 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ HIS A -3 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ THR A -2 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ ASP A -1 UNP H2B3G5 EXPRESSION TAG SEQADV 8AEJ PRO A 0 UNP H2B3G5 EXPRESSION TAG SEQRES 1 A 188 MET ARG GLY SER HIS HIS HIS HIS HIS HIS THR ASP PRO SEQRES 2 A 188 HIS GLU GLU GLU ASN ASP VAL VAL LYS GLY ASN PHE ASP SEQRES 3 A 188 ILE SER LYS ILE SER GLY ASP TRP TYR SER ILE LEU LEU SEQRES 4 A 188 ALA SER ASP ILE LYS GLU LYS ILE GLU GLU ASN GLY SER SEQRES 5 A 188 MET ARG VAL PHE VAL LYS ASP ILE GLU VAL LEU SER ASN SEQRES 6 A 188 SER SER LEU ILE PHE THR MET HIS THR LYS VAL ASN GLY SEQRES 7 A 188 LYS CYS THR LYS ILE SER LEU ILE CYS ASN LYS THR GLU SEQRES 8 A 188 LYS ASP GLY GLU TYR ASP VAL VAL HIS ASP GLY TYR ASN SEQRES 9 A 188 LEU PHE ARG ILE ILE GLU THR ALA TYR GLU ASP TYR ILE SEQRES 10 A 188 ILE PHE HIS LEU ASN ASN VAL ASN GLN GLU GLN GLU PHE SEQRES 11 A 188 GLN LEU MET GLU LEU TYR GLY ARG LYS PRO ASP VAL SER SEQRES 12 A 188 PRO LYS VAL LYS GLU LYS PHE VAL ARG TYR CYS GLN GLY SEQRES 13 A 188 MET GLU ILE PRO LYS GLU ASN ILE LEU ASP LEU THR GLN SEQRES 14 A 188 VAL ASP ARG CYS LEU GLN ALA ARG GLN SER GLU ALA ALA SEQRES 15 A 188 GLN VAL SER SER ALA GLU HET LWE A 201 11 HETNAM LWE (+)-MENTHONE FORMUL 2 LWE C10 H18 O FORMUL 3 HOH *62(H2 O) HELIX 1 AA1 ASP A 13 SER A 18 5 6 HELIX 2 AA2 ILE A 30 GLU A 35 5 6 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 THR A 155 VAL A 157 5 3 HELIX 6 AA6 CYS A 160 ARG A 164 5 5 SHEET 1 AA110 GLY A 19 ASP A 20 0 SHEET 2 AA110 PHE A 43 SER A 51 -1 O ILE A 47 N GLY A 19 SHEET 3 AA110 SER A 54 VAL A 63 -1 O HIS A 60 N PHE A 43 SHEET 4 AA110 LYS A 66 LYS A 76 -1 O THR A 68 N THR A 61 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 PHE A 93 N TYR A 83 SHEET 7 AA110 TYR A 103 VAL A 111 -1 O VAL A 111 N TYR A 90 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 2.02 CRYST1 67.075 67.075 71.985 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 0.014909 0.008608 0.000000 0.00000 SCALE2 0.000000 0.017215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013892 0.00000