HEADER PROTEIN BINDING 28-APR-20 6YVG TITLE CRYSTAL STRUCTURE OF MESI (LPG2505) FROM LEGIONELLA PNEUMOPHILA COMPND MOL_ID: 1; COMPND 2 MOLECULE: MESI (LPG2505); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA SOURCE 3 (STRAIN PHILADELPHIA 1 / ATCC 33152 / DSM 7513); SOURCE 4 ORGANISM_TAXID: 272624; SOURCE 5 GENE: LPG2505; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.A.MACHTENS,J.M.WILLERDING,S.ESCHENBURG,T.F.REUBOLD REVDAT 4 15-MAY-24 6YVG 1 REMARK REVDAT 3 01-JUL-20 6YVG 1 REMARK REVDAT 2 17-JUN-20 6YVG 1 JRNL REVDAT 1 10-JUN-20 6YVG 0 JRNL AUTH D.A.MACHTENS,J.M.WILLERDING,S.ESCHENBURG,T.F.REUBOLD JRNL TITL CRYSTAL STRUCTURE OF THE METAEFFECTOR MESI (LPG2505) FROM JRNL TITL 2 LEGIONELLA PNEUMOPHILA. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 527 696 2020 JRNL REFN ESSN 1090-2104 JRNL PMID 32423822 JRNL DOI 10.1016/J.BBRC.2020.05.027 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15647 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 783 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 44.1400 - 4.0000 1.00 2533 134 0.1490 0.1755 REMARK 3 2 4.0000 - 3.1700 1.00 2487 131 0.1771 0.2405 REMARK 3 3 3.1700 - 2.7700 1.00 2459 129 0.2310 0.2879 REMARK 3 4 2.7700 - 2.5200 1.00 2484 130 0.2337 0.2801 REMARK 3 5 2.5200 - 2.3400 1.00 2457 130 0.2477 0.2905 REMARK 3 6 2.3400 - 2.2000 1.00 2444 129 0.2874 0.3513 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.94 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6YVG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-18; 30-MAY-18; 30-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100; 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : SOLEIL; SOLEIL; SOLEIL REMARK 200 BEAMLINE : PROXIMA 2; PROXIMA 2; PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98; 2.0837; 1.0386 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M; DECTRIS REMARK 200 EIGER X 9M; DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15667 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.529 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.52 REMARK 200 R MERGE FOR SHELL (I) : 0.96000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CRANK2, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM IODIDE, 20 % W/V REMARK 280 PEG3350, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 28.45500 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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 GLY A -5 REMARK 465 ALA A -4 REMARK 465 MET A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ILE A 2 REMARK 465 SER A 277 REMARK 465 MET A 278 REMARK 465 SER A 279 REMARK 465 THR A 280 REMARK 465 ALA A 281 REMARK 465 GLY A 282 REMARK 465 LYS A 283 REMARK 465 ASP A 284 REMARK 465 ASP A 285 REMARK 465 GLU A 286 REMARK 465 ARG A 287 REMARK 465 SER A 288 REMARK 465 ILE A 289 REMARK 465 THR A 290 REMARK 465 ARG A 291 REMARK 465 PRO A 292 REMARK 465 ILE A 293 REMARK 465 ILE A 294 REMARK 465 LEU A 295 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 9 98.06 -60.91 REMARK 500 ILE A 23 91.44 -69.00 REMARK 500 LYS A 74 -71.20 -84.70 REMARK 500 PRO A 83 38.34 -81.93 REMARK 500 ASP A 84 -105.24 66.95 REMARK 500 GLN A 106 -75.09 -65.67 REMARK 500 ILE A 109 -7.86 -55.51 REMARK 500 LYS A 167 -133.27 47.67 REMARK 500 SER A 251 -118.84 55.20 REMARK 500 PHE A 274 48.07 -106.96 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 EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues IOD A 302 and IOD A REMARK 800 305 DBREF 6YVG A 1 295 UNP Q5ZSL2 Q5ZSL2_LEGPH 1 295 SEQADV 6YVG GLY A -5 UNP Q5ZSL2 EXPRESSION TAG SEQADV 6YVG ALA A -4 UNP Q5ZSL2 EXPRESSION TAG SEQADV 6YVG MET A -3 UNP Q5ZSL2 EXPRESSION TAG SEQADV 6YVG GLY A -2 UNP Q5ZSL2 EXPRESSION TAG SEQADV 6YVG GLY A -1 UNP Q5ZSL2 EXPRESSION TAG SEQADV 6YVG SER A 0 UNP Q5ZSL2 EXPRESSION TAG SEQRES 1 A 301 GLY ALA MET GLY GLY SER MET ILE LYS GLY LYS LEU MET SEQRES 2 A 301 PRO ASN SER LEU LYS ASP VAL GLN LYS LEU ILE CYS ASP SEQRES 3 A 301 GLU GLY ILE THR ASP ASN VAL ILE THR THR LEU SER ARG SEQRES 4 A 301 LEU LYS PRO PHE ASP LEU ALA MET LEU LYS ALA THR SER SEQRES 5 A 301 ASP ASN LYS VAL LYS THR LEU LEU ASP SER ASP GLU LEU SEQRES 6 A 301 LYS PRO PHE TRP VAL ASN LYS PHE ASN LYS LEU ARG LEU SEQRES 7 A 301 GLU LYS ASP HIS ILE PHE GLN PHE ARG ASN PRO ASP PRO SEQRES 8 A 301 GLN SER ARG ALA ASP PHE TYR CYS GLY TYR VAL LEU TYR SEQRES 9 A 301 LEU ALA ALA LEU LYS GLU LYS GLN LYS GLU ILE SER SER SEQRES 10 A 301 TYR TYR ASP TYR LEU ASN LEU SER PHE THR THR PHE ASN SEQRES 11 A 301 CYS PHE TYR ALA ALA GLN GLU ILE LEU THR PHE LEU ILE SEQRES 12 A 301 GLY ALA CYS LYS ASN ASP THR LYS ARG GLU ASN ILE ASP SEQRES 13 A 301 LEU LEU TYR ASN PHE VAL THR SER GLN SER THR GLN ILE SEQRES 14 A 301 GLN GLU HIS LYS THR PRO GLY CYS LEU LEU LEU ALA ASN SEQRES 15 A 301 ALA TYR PHE TYR LEU ALA GLY PHE TYR LEU SER LEU ASP SEQRES 16 A 301 LEU LYS ALA GLU SER ILE GLU CYS TYR LYS GLU CYS TRP SEQRES 17 A 301 GLY GLN LEU HIS LEU ALA GLN LEU LEU GLU THR ASP SER SEQRES 18 A 301 GLU ARG GLU ILE HIS ASN ALA TYR PHE ASN LYS GLY LEU SEQRES 19 A 301 ALA THR SER ASN ALA PHE GLY LEU ASN SER ILE SER GLU SEQRES 20 A 301 ILE LYS ALA ARG CYS LEU ASP LEU ALA SER GLU ALA LEU SEQRES 21 A 301 PRO TYR PRO ALA ARG ASN VAL MET GLU ALA ASN ALA VAL SEQRES 22 A 301 LYS THR PHE GLU ASN ARG PHE LYS ASP SER MET SER THR SEQRES 23 A 301 ALA GLY LYS ASP ASP GLU ARG SER ILE THR ARG PRO ILE SEQRES 24 A 301 ILE LEU HET EDO A 301 4 HET IOD A 302 1 HET IOD A 303 1 HET IOD A 304 1 HET IOD A 305 1 HET IOD A 306 1 HET IOD A 307 1 HET IOD A 308 1 HET IOD A 309 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM IOD IODIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 IOD 8(I 1-) FORMUL 11 HOH *45(H2 O) HELIX 1 AA1 ASN A 9 GLY A 22 1 14 HELIX 2 AA2 THR A 24 LEU A 34 1 11 HELIX 3 AA3 LYS A 35 THR A 45 1 11 HELIX 4 AA4 ASP A 47 SER A 56 1 10 HELIX 5 AA5 LEU A 59 LEU A 70 1 12 HELIX 6 AA6 SER A 87 GLU A 104 1 18 HELIX 7 AA7 GLU A 108 THR A 122 1 15 HELIX 8 AA8 CYS A 125 ASP A 143 1 19 HELIX 9 AA9 LYS A 145 GLN A 164 1 20 HELIX 10 AB1 HIS A 166 LEU A 188 1 23 HELIX 11 AB2 LEU A 190 GLU A 212 1 23 HELIX 12 AB3 SER A 215 TYR A 223 1 9 HELIX 13 AB4 GLY A 227 ASN A 232 5 6 HELIX 14 AB5 SER A 238 SER A 251 1 14 HELIX 15 AB6 GLU A 252 LEU A 254 5 3 HELIX 16 AB7 PRO A 255 PHE A 274 1 20 LINK I IOD A 302 I IOD A 305 1555 1555 3.03 SITE 1 AC1 5 ASN A 176 ASN A 232 ALA A 233 ILE A 242 SITE 2 AC1 5 CYS A 246 SITE 1 AC2 1 ALA A 244 SITE 1 AC3 1 THR A 269 SITE 1 AC4 1 IOD A 302 SITE 1 AC5 3 GLN A 209 SER A 240 IOD A 307 CRYST1 38.960 56.910 70.920 90.00 99.61 90.00 P 1 21 1 2 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 0.025667 0.000000 0.004346 0.00000 SCALE2 0.000000 0.017572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014301 0.00000