HEADER STRUCTURAL PROTEIN 23-OCT-25 9XAS TITLE CRYSTAL STRUCTURE OF SENSORY APPENDAGE PROTEIN (AGSAP2) MUTANT FROM TITLE 2 ANOPHELES GAMBIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGAP008052-PA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE SENSORY APPENDAGE PROTEIN SAP-2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANOPHELES GAMBIAE; SOURCE 3 ORGANISM_COMMON: AFRICAN MALARIA MOSQUITO; SOURCE 4 ORGANISM_TAXID: 7165; SOURCE 5 GENE: SAP-2, 1277898, AGAP_AGAP008052; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS INSECTICIDE BINDING PROTEIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.K.CHOONG,J.SIVARAMAN REVDAT 1 28-OCT-26 9XAS 0 JRNL AUTH S.BISWAS,Y.MANICKAM,C.Y.KHAI,R.GOSWAMI,S.SUKLA,R.BARBOSA, JRNL AUTH 2 S.SUNG,R.CHATURVEDI,J.A.MARQUEZ,A.CHAKI,A.SHARMA,R.DAS, JRNL AUTH 3 J.SIVARAMAN,S.CHAKRABORTI JRNL TITL STRUCTURAL INSIGHTS INTO PYRETHROID RECOGNITION BY ANOPHELES JRNL TITL 2 CHEMOSENSORY PROTEINS. JRNL REF ACS INFECT DIS. 2026 JRNL REFN ESSN 2373-8227 JRNL PMID 42673356 JRNL DOI 10.1021/ACSINFECDIS.6C00114 REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 19518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1946 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 34.4700 - 3.1700 1.00 1439 161 0.1706 0.1953 REMARK 3 2 3.1600 - 2.5100 1.00 1368 152 0.1758 0.1988 REMARK 3 3 2.5100 - 2.2000 1.00 1349 149 0.1714 0.1859 REMARK 3 4 2.1900 - 1.9900 1.00 1349 151 0.1564 0.1987 REMARK 3 5 1.9900 - 1.8500 1.00 1319 146 0.1728 0.2087 REMARK 3 6 1.8500 - 1.7400 1.00 1326 148 0.1747 0.1984 REMARK 3 7 1.7400 - 1.6500 0.99 1304 146 0.1669 0.1712 REMARK 3 8 1.6500 - 1.5800 1.00 1305 145 0.1615 0.2049 REMARK 3 9 1.5800 - 1.5200 0.99 1304 145 0.1711 0.1926 REMARK 3 10 1.5200 - 1.4700 0.99 1315 145 0.1620 0.2050 REMARK 3 11 1.4700 - 1.4200 0.95 1242 139 0.1899 0.2217 REMARK 3 12 1.4200 - 1.3800 0.88 1141 127 0.1960 0.2216 REMARK 3 13 1.3800 - 1.3500 0.81 1067 115 0.2223 0.2272 REMARK 3 14 1.3500 - 1.3100 0.57 744 77 0.3229 0.3598 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.670 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 : 0.015 804 REMARK 3 ANGLE : 1.390 1080 REMARK 3 CHIRALITY : 0.102 114 REMARK 3 PLANARITY : 0.013 142 REMARK 3 DIHEDRAL : 5.840 107 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 9XAS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1300065009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-21 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : STFC LARGE PIXEL DETECTOR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19810 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 54.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 55.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58500 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1N8V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE AND 30% REMARK 280 W/V PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.28100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.41700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.15950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.41700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.28100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.15950 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 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 1 REMARK 465 LYS A 2 REMARK 465 LEU A 3 REMARK 465 PHE A 4 REMARK 465 VAL A 5 REMARK 465 ALA A 6 REMARK 465 ILE A 7 REMARK 465 ALA A 8 REMARK 465 PHE A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 ALA A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 GLN A 18 REMARK 465 GLU A 19 REMARK 465 GLN A 20 REMARK 465 TYR A 21 REMARK 465 THR A 22 REMARK 465 ALA A 120 REMARK 465 ALA A 121 REMARK 465 ALA A 122 REMARK 465 GLY A 123 REMARK 465 ILE A 124 REMARK 465 LYS A 125 REMARK 465 LEU A 126 REMARK 465 GLU A 127 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 73 O HOH A 201 1.78 REMARK 500 O ALA A 119 O HOH A 202 2.03 REMARK 500 O HOH A 224 O HOH A 285 2.16 REMARK 500 O GLU A 117 O HOH A 203 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 275 O HOH A 288 2664 2.16 REMARK 500 O HOH A 203 O HOH A 282 1455 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 50 CB GLU A 50 CG -0.121 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 106 66.28 -155.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 9XAS A 1 127 UNP Q6H8Z3 Q6H8Z3_ANOGA 1 127 SEQADV 9XAS ALA A 77 UNP Q6H8Z3 GLU 77 ENGINEERED MUTATION SEQADV 9XAS ALA A 78 UNP Q6H8Z3 LYS 78 ENGINEERED MUTATION SEQADV 9XAS ALA A 79 UNP Q6H8Z3 GLN 79 ENGINEERED MUTATION SEQADV 9XAS ALA A 120 UNP Q6H8Z3 LYS 120 ENGINEERED MUTATION SEQADV 9XAS ALA A 121 UNP Q6H8Z3 LYS 121 ENGINEERED MUTATION SEQADV 9XAS ALA A 122 UNP Q6H8Z3 GLU 122 ENGINEERED MUTATION SEQRES 1 A 127 MET LYS LEU PHE VAL ALA ILE ALA PHE ALA LEU LEU ALA SEQRES 2 A 127 LEU ALA ALA ALA GLN GLU GLN TYR THR THR LYS TYR ASP SEQRES 3 A 127 GLY ILE ASP LEU ASP GLU ILE LEU LYS SER ASP ARG LEU SEQRES 4 A 127 PHE ASN ASN TYR PHE LYS CYS LEU MET ASP GLU GLY ARG SEQRES 5 A 127 CYS THR PRO ASP GLY ASN GLU LEU LYS LYS ILE LEU PRO SEQRES 6 A 127 GLU ALA LEU GLN THR ASN CYS GLU LYS CYS SER ALA ALA SEQRES 7 A 127 ALA ARG SER GLY ALA ILE LYS VAL ILE ASN TYR VAL ILE SEQRES 8 A 127 GLU ASN ARG LYS GLU GLN TRP ASP ALA LEU GLN LYS LYS SEQRES 9 A 127 TYR ASP PRO GLU ASN LEU TYR VAL GLU LYS TYR ARG GLU SEQRES 10 A 127 GLU ALA ALA ALA ALA GLY ILE LYS LEU GLU FORMUL 2 HOH *102(H2 O) HELIX 1 AA1 LEU A 30 SER A 36 1 7 HELIX 2 AA2 SER A 36 MET A 48 1 13 HELIX 3 AA3 THR A 54 ASN A 71 1 18 HELIX 4 AA4 SER A 76 ARG A 94 1 19 HELIX 5 AA5 ARG A 94 ASP A 106 1 13 HELIX 6 AA6 ASN A 109 TYR A 115 1 7 SHEET 1 AA1 2 LYS A 24 TYR A 25 0 SHEET 2 AA1 2 ILE A 28 ASP A 29 -1 O ILE A 28 N TYR A 25 SSBOND 1 CYS A 46 CYS A 53 1555 1555 2.06 SSBOND 2 CYS A 72 CYS A 75 1555 1555 2.07 CRYST1 34.562 44.319 54.834 90.00 90.00 90.00 P 21 21 21 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 0.028934 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018237 0.00000 CONECT 204 258 CONECT 258 204 CONECT 402 426 CONECT 426 402 MASTER 307 0 0 6 2 0 0 6 894 1 4 10 END