HEADER TRANSPORT PROTEIN 17-FEB-19 6QQ4 TITLE ODORANT-BINDING PROTEIN DMELOBP28A FROM DROSOPHILA MELANOGASTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL ODORANT-BINDING PROTEIN 28A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ODORANT-BINDING PROTEIN 28A,PHEROMONE-BINDING PROTEIN- COMPND 5 RELATED PROTEIN 5,PBPRP-5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: OBP28A, PBPRP5, CG6641; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ODORANT-BINDING PROTEIN, PHEROMONE-BINDING PROTEIN, DROSOPHILA KEYWDS 2 MELANOGASTER, OLFACTION, GUSTATION, TASTE, TRANSPORT, CARRIER, KEYWDS 3 PERIRECEPTOR EVENTS, COMPLEX, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.GONZALEZ,F.NEIERS,G.GOTTHARD,L.BRIAND REVDAT 3 24-JAN-24 6QQ4 1 REMARK REVDAT 2 30-SEP-20 6QQ4 1 JRNL REVDAT 1 18-MAR-20 6QQ4 0 JRNL AUTH D.GONZALEZ,K.RIHANI,F.NEIERS,N.POIRIER,S.FRAICHARD, JRNL AUTH 2 G.GOTTHARD,T.CHERTEMPS,M.MAIBECHE,J.F.FERVEUR,L.BRIAND JRNL TITL THE DROSOPHILA ODORANT-BINDING PROTEIN 28A IS INVOLVED IN JRNL TITL 2 THE DETECTION OF THE FLORAL ODOUR SS-IONONE. JRNL REF CELL.MOL.LIFE SCI. V. 77 2565 2020 JRNL REFN ESSN 1420-9071 JRNL PMID 31564000 JRNL DOI 10.1007/S00018-019-03300-4 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 16935 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 848 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 45.0500 - 3.6301 0.99 2745 146 0.1637 0.2108 REMARK 3 2 3.6301 - 2.8815 0.97 2644 139 0.1883 0.2055 REMARK 3 3 2.8815 - 2.5173 0.97 2661 141 0.2111 0.2881 REMARK 3 4 2.5173 - 2.2871 0.99 2698 141 0.2114 0.2696 REMARK 3 5 2.2871 - 2.1232 0.98 2667 141 0.2387 0.3037 REMARK 3 6 2.1232 - 1.9980 0.98 2672 140 0.2515 0.3036 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) : 26.170 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 : 0.007 1809 REMARK 3 ANGLE : 1.082 2421 REMARK 3 CHIRALITY : 0.038 275 REMARK 3 PLANARITY : 0.004 318 REMARK 3 DIHEDRAL : 13.760 679 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 6QQ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8 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) : 0.978 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16958 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.998 REMARK 200 RESOLUTION RANGE LOW (A) : 45.039 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.290 REMARK 200 R MERGE (I) : 0.06494 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.46 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.990 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, MRBUMP REMARK 200 STARTING MODEL: 1ORG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M SODIUM MALONATE, 0.1 M HEPES, REMARK 280 0.5% JEFFAMINE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 41.60000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 LYS A 9 CG CD CE NZ REMARK 470 GLU A 65 CG CD OE1 OE2 REMARK 470 GLU A 69 CG CD OE1 OE2 REMARK 470 ASP B 2 CG OD1 OD2 REMARK 470 GLU B 3 CG CD OE1 OE2 REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 GLU B 5 CG CD OE1 OE2 REMARK 470 GLU B 69 CG CD OE1 OE2 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 GLU B 12 CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 103 O HOH A 301 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU B 62 CA - CB - CG ANGL. DEV. = 16.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLA B 201 DBREF 6QQ4 A 2 122 UNP P54195 OB28A_DROME 23 143 DBREF 6QQ4 B 2 122 UNP P54195 OB28A_DROME 23 143 SEQRES 1 A 121 ASP GLU LYS GLU ALA LEU ALA LYS LEU MET GLU SER ALA SEQRES 2 A 121 GLU SER CYS MET PRO GLU VAL GLY ALA THR ASP ALA ASP SEQRES 3 A 121 LEU GLN GLU MET VAL LYS LYS GLN PRO ALA SER THR TYR SEQRES 4 A 121 ALA GLY LYS CYS LEU ARG ALA CYS VAL MET LYS ASN ILE SEQRES 5 A 121 GLY ILE LEU ASP ALA ASN GLY LYS LEU ASP THR GLU ALA SEQRES 6 A 121 GLY HIS GLU LYS ALA LYS GLN TYR THR GLY ASN ASP PRO SEQRES 7 A 121 ALA LYS LEU LYS ILE ALA LEU GLU ILE GLY ASP THR CYS SEQRES 8 A 121 ALA ALA ILE THR VAL PRO ASP ASP HIS CYS GLU ALA ALA SEQRES 9 A 121 GLU ALA TYR GLY THR CYS PHE ARG GLY GLU ALA LYS LYS SEQRES 10 A 121 HIS GLY LEU LEU SEQRES 1 B 121 ASP GLU LYS GLU ALA LEU ALA LYS LEU MET GLU SER ALA SEQRES 2 B 121 GLU SER CYS MET PRO GLU VAL GLY ALA THR ASP ALA ASP SEQRES 3 B 121 LEU GLN GLU MET VAL LYS LYS GLN PRO ALA SER THR TYR SEQRES 4 B 121 ALA GLY LYS CYS LEU ARG ALA CYS VAL MET LYS ASN ILE SEQRES 5 B 121 GLY ILE LEU ASP ALA ASN GLY LYS LEU ASP THR GLU ALA SEQRES 6 B 121 GLY HIS GLU LYS ALA LYS GLN TYR THR GLY ASN ASP PRO SEQRES 7 B 121 ALA LYS LEU LYS ILE ALA LEU GLU ILE GLY ASP THR CYS SEQRES 8 B 121 ALA ALA ILE THR VAL PRO ASP ASP HIS CYS GLU ALA ALA SEQRES 9 B 121 GLU ALA TYR GLY THR CYS PHE ARG GLY GLU ALA LYS LYS SEQRES 10 B 121 HIS GLY LEU LEU HET 1PE A 201 16 HET MLA B 201 7 HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM MLA MALONIC ACID HETSYN 1PE PEG400 HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 3 1PE C10 H22 O6 FORMUL 4 MLA C3 H4 O4 FORMUL 5 HOH *168(H2 O) HELIX 1 AA1 ASP A 2 MET A 18 1 17 HELIX 2 AA2 PRO A 19 GLY A 22 5 4 HELIX 3 AA3 THR A 24 LYS A 33 1 10 HELIX 4 AA4 THR A 39 GLY A 54 1 16 HELIX 5 AA5 ALA A 66 GLY A 76 1 11 HELIX 6 AA6 ASP A 78 ALA A 93 1 16 HELIX 7 AA7 ASP A 100 HIS A 119 1 20 HELIX 8 AA8 LYS B 4 VAL B 21 1 18 HELIX 9 AA9 THR B 24 LYS B 33 1 10 HELIX 10 AB1 THR B 39 ILE B 53 1 15 HELIX 11 AB2 ASP B 63 GLY B 76 1 14 HELIX 12 AB3 ASP B 78 ALA B 80 5 3 HELIX 13 AB4 LYS B 81 ALA B 94 1 14 HELIX 14 AB5 ASP B 100 HIS B 119 1 20 SSBOND 1 CYS A 17 CYS A 48 1555 1555 2.05 SSBOND 2 CYS A 44 CYS A 102 1555 1555 2.05 SSBOND 3 CYS A 92 CYS A 111 1555 1555 2.04 SSBOND 4 CYS B 17 CYS B 48 1555 1555 2.07 SSBOND 5 CYS B 44 CYS B 102 1555 1555 2.05 SSBOND 6 CYS B 92 CYS B 111 1555 1555 2.04 SITE 1 AC1 6 ARG A 46 TYR A 74 ALA A 85 GLY A 89 SITE 2 AC1 6 PHE A 112 ARG A 113 SITE 1 AC2 7 LYS B 34 ARG B 46 LYS B 70 TYR B 74 SITE 2 AC2 7 GLU B 106 GLY B 109 ARG B 113 CRYST1 34.500 83.200 45.600 90.00 99.00 90.00 P 1 21 1 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 0.028986 0.000000 0.004591 0.00000 SCALE2 0.000000 0.012019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022203 0.00000