HEADER TRANSPORT PROTEIN 18-DEC-09 3L47 TITLE CRYSTAL STRUCTURE OF THE ANOPHELES GAMBIAE ODORANT-BINDING PROTEIN 22A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ODORANT BINDING PROTEIN (AGAP010409-PA); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AGAMOBP22A, UNP RESIDUES 22-144; COMPND 5 SYNONYM: ODORANT-BINDING PROTEIN OBPJJ83B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANOPHELES GAMBIAE; SOURCE 3 ORGANISM_COMMON: AFRICAN MALARIA MOSQUITO; SOURCE 4 ORGANISM_TAXID: 180454; SOURCE 5 STRAIN: PEST; SOURCE 6 GENE: AGAMOBP22A, AGAP010409, OBP22, OBPJJ83B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-STAR-PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALL ALPHA HELIX, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.REN,S.ZHANG REVDAT 5 07-MAR-18 3L47 1 REMARK REVDAT 4 01-NOV-17 3L47 1 REMARK REVDAT 3 16-NOV-11 3L47 1 VERSN HETATM REVDAT 2 16-FEB-11 3L47 1 COMPND REMARK REVDAT 1 12-JAN-11 3L47 0 JRNL AUTH H.REN,G.YANG,G.WINBERG,L.TURIN,A.MERSHIN,S.ZHANG JRNL TITL THE CRYSTAL STRUCTURES OF AN ANOPHELES GAMBIAE JRNL TITL 2 ODORANT-BINDING PROTEIN AGAMOBP22A AND COMPLEXES WITH BOUND JRNL TITL 3 ODORANTS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 4069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 408 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 29.8300 - 3.6130 0.99 1253 140 0.1760 0.2130 REMARK 3 2 3.6130 - 2.8680 0.99 1211 135 0.1730 0.2160 REMARK 3 3 2.8680 - 2.5060 0.97 1197 133 0.1950 0.2640 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 : 0.35 REMARK 3 B_SOL : 32.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 2.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.46600 REMARK 3 B22 (A**2) : -1.11400 REMARK 3 B33 (A**2) : 1.39800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.58300 REMARK 3 B23 (A**2) : 0.00000 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 : 0.010 892 REMARK 3 ANGLE : 1.156 1204 REMARK 3 CHIRALITY : 0.081 127 REMARK 3 PLANARITY : 0.004 164 REMARK 3 DIHEDRAL : 23.034 318 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 3L47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000056811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4107 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: RESOLVE 2.13, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM CITRATE TRIBASIC, MPD, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.93550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.96000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.93550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.96000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 174 LIES ON A SPECIAL POSITION. 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 ALA A 22 REMARK 465 ASP A 23 REMARK 465 ASN A 24 REMARK 465 ASN A 25 REMARK 465 GLU A 26 REMARK 465 GLN A 136 REMARK 465 ASN A 137 REMARK 465 ASN A 138 REMARK 465 ASN A 139 REMARK 465 ASN A 140 REMARK 465 ALA A 141 REMARK 465 THR A 142 REMARK 465 SER A 143 REMARK 465 GLU A 144 REMARK 465 LEU A 145 REMARK 465 VAL A 146 REMARK 465 PRO A 147 REMARK 465 ARG A 148 REMARK 465 GLY A 149 REMARK 465 SER A 150 REMARK 465 SER A 151 REMARK 465 GLY A 152 REMARK 465 GLU A 153 REMARK 465 LEU A 154 REMARK 465 TRP A 155 REMARK 465 SER A 156 REMARK 465 HIS A 157 REMARK 465 PRO A 158 REMARK 465 GLN A 159 REMARK 465 PHE A 160 REMARK 465 GLU A 161 REMARK 465 LYS A 162 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 110 61.82 39.54 REMARK 500 MET A 134 20.16 -77.52 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 AU A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3L4A RELATED DB: PDB REMARK 900 AGAMOBP22A_NATIVE REMARK 900 RELATED ID: 3L4L RELATED DB: PDB REMARK 900 AGAMOBP22A_BENZALDEHYDE REMARK 900 RELATED ID: 3L5G RELATED DB: PDB REMARK 900 AGAMOBP22A_ CYCLOHEXANONE REMARK 900 RELATED ID: 3PJI RELATED DB: PDB REMARK 900 AGAMOBP22A AT 1.7 ANGSTROM IN THE OPEN STATUS FOR LIGAND BINDING DBREF 3L47 A 22 144 UNP Q7PGA3 Q7PGA3_ANOGA 22 144 SEQADV 3L47 LEU A 145 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 VAL A 146 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 PRO A 147 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 ARG A 148 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 GLY A 149 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 SER A 150 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 SER A 151 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 GLY A 152 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 GLU A 153 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 LEU A 154 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 TRP A 155 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 SER A 156 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 HIS A 157 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 PRO A 158 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 GLN A 159 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 PHE A 160 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 GLU A 161 UNP Q7PGA3 EXPRESSION TAG SEQADV 3L47 LYS A 162 UNP Q7PGA3 EXPRESSION TAG SEQRES 1 A 141 ALA ASP ASN ASN GLU SER VAL ILE GLU SER CYS SER ASN SEQRES 2 A 141 ALA VAL GLN GLY ALA ALA ASN ASP GLU LEU LYS VAL HIS SEQRES 3 A 141 TYR ARG ALA ASN GLU PHE PRO ASP ASP PRO VAL THR HIS SEQRES 4 A 141 CYS PHE VAL ARG CYS ILE GLY LEU GLU LEU ASN LEU TYR SEQRES 5 A 141 ASP ASP LYS TYR GLY VAL ASP LEU GLN ALA ASN TRP GLU SEQRES 6 A 141 ASN LEU GLY ASN SER ASP ASP ALA ASP GLU GLU PHE VAL SEQRES 7 A 141 ALA LYS HIS ARG ALA CYS LEU GLU ALA LYS ASN LEU GLU SEQRES 8 A 141 THR ILE GLU ASP LEU CYS GLU ARG ALA TYR SER ALA PHE SEQRES 9 A 141 GLN CYS LEU ARG GLU ASP TYR GLU MET TYR GLN ASN ASN SEQRES 10 A 141 ASN ASN ALA THR SER GLU LEU VAL PRO ARG GLY SER SER SEQRES 11 A 141 GLY GLU LEU TRP SER HIS PRO GLN PHE GLU LYS HET AU A 1 1 HET AU A 2 1 HETNAM AU GOLD ION FORMUL 2 AU 2(AU 1+) FORMUL 4 HOH *39(H2 O) HELIX 1 1 SER A 27 VAL A 36 1 10 HELIX 2 2 ASN A 41 ALA A 50 1 10 HELIX 3 3 ASP A 56 LEU A 70 1 15 HELIX 4 4 ASP A 80 LEU A 88 1 9 HELIX 5 5 ASP A 95 LYS A 109 1 15 HELIX 6 6 ASN A 110 ILE A 114 5 5 HELIX 7 7 ASP A 116 GLN A 126 1 11 HELIX 8 8 LEU A 128 MET A 134 1 7 SHEET 1 A 2 TYR A 73 ASP A 74 0 SHEET 2 A 2 GLY A 78 VAL A 79 -1 O GLY A 78 N ASP A 74 SSBOND 1 CYS A 32 CYS A 65 1555 1555 2.04 SSBOND 2 CYS A 61 CYS A 118 1555 1555 2.04 SSBOND 3 CYS A 105 CYS A 127 1555 1555 2.02 LINK ND1 HIS A 60 AU AU A 1 1555 1555 2.20 LINK NE2 HIS A 47 AU AU A 2 1555 1555 2.40 SITE 1 AC1 2 PRO A 57 HIS A 60 SITE 1 AC2 1 HIS A 47 CRYST1 71.871 37.920 43.889 90.00 98.92 90.00 C 1 2 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 0.013914 0.000000 0.002183 0.00000 SCALE2 0.000000 0.026371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023063 0.00000