HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 12-DEC-14 4RXV TITLE THE CRYSTAL STRUCTURE OF THE N-TERMINAL FRAGMENT OF UNCHARACTERIZED TITLE 2 PROTEIN FROM LEGIONELLA PNEUMOPHILA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN LPG0944; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. SOURCE 3 PHILADELPHIA 1; SOURCE 4 ORGANISM_TAXID: 272624; SOURCE 5 STRAIN: PHILADELPHIA 1 / ATCC 33152 / DSM 7513; SOURCE 6 GENE: LPG0944; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MCSG, PSI-BIOLOGY, STRUCTURAL GENOMICS, MIDWEST CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR B.NOCEK,M.CUFF,E.EVDOKIMOVA,O.EGOROVA,A.JOACHIMIAK,A.ENSMINGER, AUTHOR 2 A.SAVCHENKO,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 3 28-FEB-24 4RXV 1 SEQADV REVDAT 2 04-JAN-17 4RXV 1 JRNL REVDAT 1 08-APR-15 4RXV 0 JRNL AUTH M.L.URBANUS,A.T.QUAILE,P.J.STOGIOS,M.MORAR,C.RAO,R.DI LEO, JRNL AUTH 2 E.EVDOKIMOVA,M.LAM,C.OATWAY,M.E.CUFF,J.OSIPIUK,K.MICHALSKA, JRNL AUTH 3 B.P.NOCEK,M.TAIPALE,A.SAVCHENKO,A.W.ENSMINGER JRNL TITL DIVERSE MECHANISMS OF METAEFFECTOR ACTIVITY IN AN JRNL TITL 2 INTRACELLULAR BACTERIAL PATHOGEN, LEGIONELLA PNEUMOPHILA. JRNL REF MOL SYST BIOL V. 12 893 2016 JRNL REFN ESSN 1744-4292 JRNL PMID 27986836 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1834) 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 62763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3177 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 37.8435 - 3.1254 0.97 2855 161 0.1401 0.1315 REMARK 3 2 3.1254 - 2.4809 1.00 2893 168 0.1359 0.1410 REMARK 3 3 2.4809 - 2.1673 1.00 2868 169 0.1233 0.1258 REMARK 3 4 2.1673 - 1.9692 1.00 2871 150 0.1145 0.1332 REMARK 3 5 1.9692 - 1.8280 1.00 2909 150 0.1108 0.1279 REMARK 3 6 1.8280 - 1.7203 1.00 2871 158 0.1085 0.1298 REMARK 3 7 1.7203 - 1.6341 1.00 2866 156 0.1052 0.1346 REMARK 3 8 1.6341 - 1.5630 1.00 2899 151 0.1060 0.1375 REMARK 3 9 1.5630 - 1.5028 1.00 2891 143 0.1019 0.1380 REMARK 3 10 1.5028 - 1.4509 1.00 2874 139 0.1074 0.1364 REMARK 3 11 1.4509 - 1.4056 1.00 2846 153 0.1087 0.1422 REMARK 3 12 1.4056 - 1.3654 1.00 2897 171 0.1111 0.1570 REMARK 3 13 1.3654 - 1.3294 1.00 2883 131 0.1196 0.1510 REMARK 3 14 1.3294 - 1.2970 1.00 2863 160 0.1148 0.1498 REMARK 3 15 1.2970 - 1.2675 1.00 2876 159 0.1207 0.1721 REMARK 3 16 1.2675 - 1.2405 1.00 2833 151 0.1215 0.1657 REMARK 3 17 1.2405 - 1.2157 1.00 2923 136 0.1249 0.1489 REMARK 3 18 1.2157 - 1.1928 0.94 2664 157 0.1379 0.1746 REMARK 3 19 1.1928 - 1.1715 0.80 2326 112 0.1468 0.1725 REMARK 3 20 1.1715 - 1.1516 0.67 1910 98 0.1601 0.1737 REMARK 3 21 1.1516 - 1.1330 0.55 1594 80 0.1672 0.1905 REMARK 3 22 1.1330 - 1.1156 0.43 1232 58 0.2035 0.2256 REMARK 3 23 1.1156 - 1.0992 0.33 942 66 0.2182 0.2413 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.450 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 : 0.010 1921 REMARK 3 ANGLE : 1.365 2634 REMARK 3 CHIRALITY : 0.074 283 REMARK 3 PLANARITY : 0.008 357 REMARK 3 DIHEDRAL : 15.123 731 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 4RXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000087930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62764 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.099 REMARK 200 RESOLUTION RANGE LOW (A) : 37.821 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.05000 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: HKL-3000, MLPHARE, DM, CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 0.1 M NACL, REMARK 280 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 34.46950 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 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 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 ARG A 149 CG CD NE CZ NH1 NH2 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 ALA A 183 -29.19 -154.27 REMARK 500 ALA A 183 -29.19 -153.70 REMARK 500 ALA A 185 60.86 66.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MCSG-APC108062 RELATED DB: TARGETTRACK DBREF 4RXV A 1 228 UNP Q5ZWY9 Q5ZWY9_LEGPH 1 228 SEQADV 4RXV GLY A 0 UNP Q5ZWY9 EXPRESSION TAG SEQRES 1 A 229 GLY MET ALA ILE ALA PRO GLN GLN ILE GLN GLU ARG LEU SEQRES 2 A 229 LYS GLN GLU GLN TYR GLN LYS PHE VAL VAL ALA ASP ILE SEQRES 3 A 229 GLY ASN PHE PRO HIS CYS LEU ALA GLN THR PRO GLU GLY SEQRES 4 A 229 ILE ALA SER GLY GLN ARG TYR GLN LYS TYR SER THR ASN SEQRES 5 A 229 SER LEU SER ARG THR PRO PRO PHE SER GLN TRP GLY ALA SEQRES 6 A 229 PRO GLN LEU LEU THR PRO LYS SER ALA GLN GLU TYR ILE SEQRES 7 A 229 LYS PHE ALA GLN GLN ARG ASN LYS LYS SER SER PHE LYS SEQRES 8 A 229 ILE ASP GLY GLU ALA VAL ARG VAL SER GLU CYS SER ASN SEQRES 9 A 229 PHE ALA TYR HIS SER ALA GLY VAL LEU LEU ASP ASP PRO SEQRES 10 A 229 GLN ILE ARG THR GLN TYR ASP VAL ALA VAL ILE GLY SER SEQRES 11 A 229 MET HIS SER ASN GLY ARG TYR LEU HIS ASN ILE THR LEU SEQRES 12 A 229 LEU VAL PRO LYS GLY SER ARG LEU PRO GLN PRO PRO GLU SEQRES 13 A 229 GLN LEU THR ALA GLU VAL PHE PRO ILE GLY THR LEU ILE SEQRES 14 A 229 VAL ASP PRO TRP ALA VAL GLY MET GLY HIS PRO PRO GLU SEQRES 15 A 229 GLN ALA LEU ALA ILE PRO LYS GLU GLN PHE ALA TYR ASN SEQRES 16 A 229 ARG SER LEU PHE PRO ALA THR VAL ASN TYR GLN SER ALA SEQRES 17 A 229 LEU ASP GLU SER LEU THR SER THR ARG THR GLY GLN LEU SEQRES 18 A 229 THR PRO TYR THR GLY THR PRO SER FORMUL 2 HOH *297(H2 O) HELIX 1 1 ALA A 4 GLN A 14 1 11 HELIX 2 2 GLU A 15 PHE A 20 5 6 HELIX 3 3 ASP A 24 LEU A 32 5 9 HELIX 4 4 THR A 35 THR A 50 1 16 HELIX 5 5 ASN A 51 THR A 56 5 6 HELIX 6 6 PRO A 58 ALA A 64 1 7 HELIX 7 7 SER A 72 ASN A 84 1 13 HELIX 8 8 ASN A 103 ASP A 114 1 12 HELIX 9 9 ASP A 115 GLN A 121 1 7 HELIX 10 10 THR A 158 PHE A 162 5 5 HELIX 11 11 ASP A 170 MET A 176 1 7 HELIX 12 12 PRO A 179 GLN A 182 5 4 HELIX 13 13 PRO A 187 PHE A 191 5 5 HELIX 14 14 ALA A 207 ASP A 209 5 3 SHEET 1 A 2 VAL A 21 VAL A 22 0 SHEET 2 A 2 VAL A 98 SER A 99 1 O SER A 99 N VAL A 21 SHEET 1 B 2 LYS A 90 ILE A 91 0 SHEET 2 B 2 GLU A 94 ALA A 95 -1 O GLU A 94 N ILE A 91 SHEET 1 C 5 LEU A 184 ILE A 186 0 SHEET 2 C 5 LEU A 167 VAL A 169 -1 N ILE A 168 O ILE A 186 SHEET 3 C 5 ARG A 135 PRO A 145 -1 N THR A 141 O VAL A 169 SHEET 4 C 5 TYR A 122 SER A 132 -1 N SER A 132 O ARG A 135 SHEET 5 C 5 THR A 201 GLN A 205 -1 O THR A 201 N GLY A 128 CISPEP 1 PRO A 57 PRO A 58 0 4.21 CISPEP 2 PRO A 153 PRO A 154 0 8.57 CISPEP 3 PHE A 198 PRO A 199 0 -0.30 CRYST1 33.515 68.939 40.947 90.00 112.53 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 0.029837 0.000000 0.012377 0.00000 SCALE2 0.000000 0.014506 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026440 0.00000