HEADER PROTEIN BINDING 28-JUN-20 6XL7 TITLE STRUCTURE OF A MOSQUITO COMPLEMENT INHIBITOR FROM ANOPHELES FREEBORNI COMPND MOL_ID: 1; COMPND 2 MOLECULE: SG7.AF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANOPHELES FREEBORNI; SOURCE 3 ORGANISM_TAXID: 7170; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: PLYSS KEYWDS INHIBITOR, COMPLEMENT, ALTERNATIVE PATHWAY, C3BBB, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.F.ANDERSEN,E.STRAYER REVDAT 3 03-APR-24 6XL7 1 REMARK REVDAT 2 14-JUL-21 6XL7 1 JRNL REVDAT 1 05-MAY-21 6XL7 0 JRNL AUTH E.C.STRAYER,S.LU,J.RIBEIRO,J.F.ANDERSEN JRNL TITL SALIVARY COMPLEMENT INHIBITORS FROM MOSQUITOES: STRUCTURE JRNL TITL 2 AND MECHANISM OF ACTION. JRNL REF J.BIOL.CHEM. V. 296 00083 2020 JRNL REFN ESSN 1083-351X JRNL PMID 33199367 JRNL DOI 10.1074/JBC.RA120.015230 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.F.MENDES-SOUSA,D.C.QUEIROZ,V.F.VALE,J.M.RIBEIRO, REMARK 1 AUTH 2 J.G.VALENZUELA,N.F.GONTIJO,J.F.ANDERSEN REMARK 1 TITL AN INHIBITOR OF THE ALTERNATIVE PATHWAY OF COMPLEMENT IN REMARK 1 TITL 2 SALIVA OF NEW WORLD ANOPHELINE MOSQUITOES. REMARK 1 REF J. IMMUNOL. V. 197 599 2016 REMARK 1 REFN ESSN 1550-6606 REMARK 1 PMID 27307559 REMARK 1 DOI 10.4049/JIMMUNOL.1600020 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 32663 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1598 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 31.4300 - 3.1600 1.00 3088 144 0.1804 0.1935 REMARK 3 2 3.1600 - 2.5100 1.00 2932 134 0.1839 0.1675 REMARK 3 3 2.5100 - 2.1900 1.00 2883 156 0.1640 0.1766 REMARK 3 4 2.1900 - 1.9900 1.00 2859 144 0.1697 0.2004 REMARK 3 5 1.9900 - 1.8500 1.00 2835 163 0.1787 0.2036 REMARK 3 6 1.8500 - 1.7400 1.00 2835 145 0.1899 0.2179 REMARK 3 7 1.7400 - 1.6500 1.00 2825 132 0.1803 0.2225 REMARK 3 8 1.6500 - 1.5800 0.99 2809 148 0.1799 0.2102 REMARK 3 9 1.5800 - 1.5200 0.99 2804 148 0.1796 0.1933 REMARK 3 10 1.5200 - 1.4700 0.98 2762 141 0.1872 0.1945 REMARK 3 11 1.4700 - 1.4200 0.87 2433 143 0.2178 0.2375 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.33 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 : 0.005 1052 REMARK 3 ANGLE : 0.855 1427 REMARK 3 CHIRALITY : 0.077 157 REMARK 3 PLANARITY : 0.005 178 REMARK 3 DIHEDRAL : 26.267 407 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 119) REMARK 3 ORIGIN FOR THE GROUP (A): 27.3719 0.9709 53.6677 REMARK 3 T TENSOR REMARK 3 T11: 0.0865 T22: 0.0791 REMARK 3 T33: 0.0678 T12: 0.0121 REMARK 3 T13: -0.0022 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.4778 L22: 4.7739 REMARK 3 L33: 0.6024 L12: 0.4736 REMARK 3 L13: -0.0843 L23: 0.6918 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: -0.0223 S13: -0.0410 REMARK 3 S21: 0.1196 S22: 0.0425 S23: -0.1155 REMARK 3 S31: 0.0502 S32: -0.0147 S33: -0.0174 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 6XL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32895 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 31.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.92 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.22200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.340 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.17 REMARK 200 STARTING MODEL: ALBICIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULFATE, 0.1 M TRIS REMARK 280 HCL, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 23.04000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.99000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.52000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.99000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.99000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.56000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.99000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.99000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.52000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.99000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.99000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.56000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.04000 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 310 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 315 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 511 LIES ON A SPECIAL POSITION. 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 LEU A 37 -57.87 -129.12 REMARK 500 SER A 78 -104.76 -122.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 522 DISTANCE = 6.67 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 205 DBREF 6XL7 A 1 119 PDB 6XL7 6XL7 1 119 SEQRES 1 A 119 ALA ARG LYS HIS VAL GLN GLU LEU LEU LYS THR PHE ARG SEQRES 2 A 119 ARG ILE ASP PHE ASP GLU THR ARG LYS SER VAL TYR LEU SEQRES 3 A 119 GLN SER ALA LYS PHE GLY VAL GLN SER GLN LEU ARG GLU SEQRES 4 A 119 PRO LEU THR LYS LYS VAL LEU ASN TYR TRP ASP ASP VAL SEQRES 5 A 119 LYS LEU SER LYS THR CYS LEU ASP ARG MET VAL THR LYS SEQRES 6 A 119 VAL ASN ASP VAL LYS GLU THR PHE TYR ALA GLY PHE SER SEQRES 7 A 119 TYR ALA CYS GLU SER HIS ASN GLN TYR SER VAL ASP CYS SEQRES 8 A 119 LEU GLU ALA ALA LYS PRO SER TYR LEU THR ALA LEU GLY SEQRES 9 A 119 GLU ILE ARG GLY GLU THR GLU LYS CYS LEU THR THR ARG SEQRES 10 A 119 LEU LYS HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET CL A 205 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 CL CL 1- FORMUL 7 HOH *222(H2 O) HELIX 1 AA1 ALA A 1 ARG A 14 1 14 HELIX 2 AA2 LYS A 22 LEU A 37 1 16 HELIX 3 AA3 LEU A 37 ASN A 47 1 11 HELIX 4 AA4 SER A 55 SER A 78 1 24 HELIX 5 AA5 SER A 88 LEU A 114 1 27 SHEET 1 AA1 2 LYS A 53 LEU A 54 0 SHEET 2 AA1 2 THR A 115 THR A 116 -1 O THR A 116 N LYS A 53 SSBOND 1 CYS A 58 CYS A 113 1555 1555 2.06 SSBOND 2 CYS A 81 CYS A 91 1555 1555 2.09 SITE 1 AC1 5 LYS A 10 ARG A 13 ARG A 14 HOH A 304 SITE 2 AC1 5 HOH A 450 SITE 1 AC2 3 LYS A 22 SER A 23 HOH A 308 SITE 1 AC3 8 ASP A 18 ARG A 21 GLN A 34 ARG A 38 SITE 2 AC3 8 TYR A 74 HOH A 320 HOH A 335 HOH A 388 SITE 1 AC4 5 SER A 55 LYS A 56 THR A 57 HOH A 325 SITE 2 AC4 5 HOH A 387 SITE 1 AC5 1 LYS A 10 CRYST1 85.980 85.980 46.080 90.00 90.00 90.00 P 41 21 2 8 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 0.011631 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021701 0.00000