HEADER LIGASE 18-NOV-14 4WZ0 TITLE CRYSTAL STRUCTURE OF U-BOX 1 OF LUBX / LEGU2 / LPP2887 FROM LEGIONELLA TITLE 2 PNEUMOPHILA STR. PARIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE LUBX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 9-117; COMPND 5 SYNONYM: LEGIONELLA U-BOX PROTEIN; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA (STRAIN PARIS); SOURCE 3 ORGANISM_TAXID: 297246; SOURCE 4 STRAIN: PARIS; SOURCE 5 GENE: LUBX, LPP2887; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: P15TV-LIC KEYWDS ALPHA/BETA PROTEIN, EFFECTOR, STRUCTURAL GENOMICS, PSI-BIOLOGY, MCSG, KEYWDS 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,A.T.QUAILE,T.SKARINA,A.STEIN,R.DI LEO,V.YIM,A.SAVCHENKO, AUTHOR 2 A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 6 30-OCT-24 4WZ0 1 REMARK REVDAT 5 04-DEC-19 4WZ0 1 REMARK REVDAT 4 20-SEP-17 4WZ0 1 JRNL REMARK REVDAT 3 19-AUG-15 4WZ0 1 JRNL REVDAT 2 29-JUL-15 4WZ0 1 JRNL REVDAT 1 14-JAN-15 4WZ0 0 JRNL AUTH A.T.QUAILE,M.L.URBANUS,P.J.STOGIOS,B.NOCEK,T.SKARINA, JRNL AUTH 2 A.W.ENSMINGER,A.SAVCHENKO JRNL TITL MOLECULAR CHARACTERIZATION OF LUBX: FUNCTIONAL DIVERGENCE OF JRNL TITL 2 THE U-BOX FOLD BY LEGIONELLA PNEUMOPHILA. JRNL REF STRUCTURE V. 23 1459 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 26146184 JRNL DOI 10.1016/J.STR.2015.05.020 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.210 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 9941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 995 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 45.3227 - 3.7373 0.97 1385 155 0.2184 0.2694 REMARK 3 2 3.7373 - 2.9666 0.97 1309 145 0.2137 0.2367 REMARK 3 3 2.9666 - 2.5917 0.97 1294 144 0.2470 0.2530 REMARK 3 4 2.5917 - 2.3547 0.97 1276 142 0.2438 0.3093 REMARK 3 5 2.3547 - 2.1859 0.92 1221 136 0.2645 0.3465 REMARK 3 6 2.1859 - 2.0571 0.95 1247 138 0.2490 0.2986 REMARK 3 7 2.0571 - 1.9540 0.92 1214 135 0.2744 0.3628 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.100 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 : 0.009 936 REMARK 3 ANGLE : 1.168 1278 REMARK 3 CHIRALITY : 0.046 146 REMARK 3 PLANARITY : 0.006 165 REMARK 3 DIHEDRAL : 12.490 374 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESI 9:89 REMARK 3 ORIGIN FOR THE GROUP (A): 61.0697 29.4945 15.8488 REMARK 3 T TENSOR REMARK 3 T11: 0.2127 T22: 0.1681 REMARK 3 T33: 0.1895 T12: 0.0018 REMARK 3 T13: 0.0262 T23: 0.0309 REMARK 3 L TENSOR REMARK 3 L11: 3.3847 L22: 5.0354 REMARK 3 L33: 3.2633 L12: 2.2284 REMARK 3 L13: 0.6008 L23: 0.4695 REMARK 3 S TENSOR REMARK 3 S11: 0.0494 S12: -0.0346 S13: -0.2639 REMARK 3 S21: -0.0260 S22: -0.0561 S23: -0.1290 REMARK 3 S31: 0.5658 S32: -0.1841 S33: 0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESI 90:117 REMARK 3 ORIGIN FOR THE GROUP (A): 83.7405 40.4867 23.1617 REMARK 3 T TENSOR REMARK 3 T11: 0.1471 T22: 0.2640 REMARK 3 T33: 0.1915 T12: 0.0087 REMARK 3 T13: 0.0245 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 6.6712 L22: 2.6005 REMARK 3 L33: 7.7559 L12: 3.3714 REMARK 3 L13: 6.3908 L23: 3.2240 REMARK 3 S TENSOR REMARK 3 S11: 0.2115 S12: 0.5614 S13: -0.0609 REMARK 3 S21: 0.1169 S22: 0.0770 S23: -0.2581 REMARK 3 S31: 0.2899 S32: 0.8519 S33: -0.2778 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 4WZ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792063 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10142 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ~30 MG PROTEIN, 0.25 M AMMONIUM REMARK 280 SULFATE, 0.1 M IMIDAZOLE PH 7.8, 28% PEG 8K, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 20.28100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.28100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.31050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.31050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.28100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.31050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 20.28100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.31050 REMARK 290 SMTRY3 8 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 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 CZ ARG A 95 NH2 ARG A 95 3755 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WZ1 RELATED DB: PDB REMARK 900 U-BOX 2 (WILD-TYPE) REMARK 900 RELATED ID: 4WZ2 RELATED DB: PDB REMARK 900 U-BOX 2, ILE175MET MUTANT REMARK 900 RELATED ID: 4WZ3 RELATED DB: PDB REMARK 900 U-BOX 1 IN COMPLEX WITH UBE2D2 REMARK 900 RELATED ID: MCSG-APC108251 RELATED DB: TARGETTRACK DBREF 4WZ0 A 17 117 UNP Q5X159 LUBX_LEGPA 17 117 SEQADV 4WZ0 ILE A 9 UNP Q5X159 EXPRESSION TAG SEQADV 4WZ0 ASP A 10 UNP Q5X159 EXPRESSION TAG SEQADV 4WZ0 HIS A 11 UNP Q5X159 EXPRESSION TAG SEQADV 4WZ0 LYS A 12 UNP Q5X159 EXPRESSION TAG SEQADV 4WZ0 SER A 13 UNP Q5X159 EXPRESSION TAG SEQADV 4WZ0 LYS A 14 UNP Q5X159 EXPRESSION TAG SEQADV 4WZ0 TYR A 15 UNP Q5X159 EXPRESSION TAG SEQADV 4WZ0 LEU A 16 UNP Q5X159 EXPRESSION TAG SEQRES 1 A 109 ILE ASP HIS LYS SER LYS TYR LEU ARG GLU ALA ALA LEU SEQRES 2 A 109 GLU ALA ASN LEU SER HIS PRO GLU THR THR PRO THR MSE SEQRES 3 A 109 LEU THR CSD PRO ILE ASP SER GLY PHE LEU LYS ASP PRO SEQRES 4 A 109 VAL ILE THR PRO GLU GLY PHE VAL TYR ASN LYS SER SER SEQRES 5 A 109 ILE LEU LYS TRP LEU GLU THR LYS LYS GLU ASP PRO GLN SEQRES 6 A 109 SER ARG LYS PRO LEU THR ALA LYS ASP LEU GLN PRO PHE SEQRES 7 A 109 PRO GLU LEU LEU ILE ILE VAL ASN ARG PHE VAL GLU THR SEQRES 8 A 109 GLN THR ASN TYR GLU LYS LEU LYS ASN ARG LEU VAL GLN SEQRES 9 A 109 ASN ALA ARG VAL ALA MODRES 4WZ0 MSE A 34 MET MODIFIED RESIDUE MODRES 4WZ0 CSD A 37 CYS MODIFIED RESIDUE HET MSE A 34 8 HET CSD A 37 13 HETNAM MSE SELENOMETHIONINE HETNAM CSD 3-SULFINOALANINE HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 HOH *143(H2 O) HELIX 1 AA1 ASP A 10 SER A 26 1 17 HELIX 2 AA2 PRO A 32 THR A 36 5 5 HELIX 3 AA3 LYS A 58 LYS A 68 1 11 HELIX 4 AA4 THR A 79 LEU A 83 5 5 HELIX 5 AA5 GLU A 88 ALA A 117 1 30 SHEET 1 AA1 3 VAL A 55 ASN A 57 0 SHEET 2 AA1 3 PRO A 47 ILE A 49 -1 N VAL A 48 O TYR A 56 SHEET 3 AA1 3 GLN A 84 PRO A 85 -1 O GLN A 84 N ILE A 49 LINK C THR A 33 N MSE A 34 1555 1555 1.33 LINK C MSE A 34 N LEU A 35 1555 1555 1.33 LINK C THR A 36 N CSD A 37 1555 1555 1.33 LINK C CSD A 37 N PRO A 38 1555 1555 1.33 CRYST1 75.334 90.621 40.562 90.00 90.00 90.00 C 2 2 21 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 0.013274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024654 0.00000