HEADER TRANSFERASE 03-JUN-14 4TN5 TITLE CRYSTAL STRUCTURE OF PREDICTED FRUCTOSE SPECIFIC IIB FROM ESCHERICHIA TITLE 2 COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRUCTOSE-LIKE PHOSPHOTRANSFERASE ENZYME IIB COMPONENT 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PTS SYSTEM FRUCTOSE-LIKE EIIB COMPONENT 3; COMPND 5 EC: 2.7.1.69; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: FRWD, YIJN, B3953, JW3925; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IIB, EIIB(FRUC), ALPHA/BETA, PHOSPHORYL GROUP TRANSFERASE, EIIA, KEYWDS 2 EIIC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.KIM,D.H.SHIN REVDAT 1 10-JUN-15 4TN5 0 SPRSDE 10-JUN-15 4TN5 4JXD JRNL AUTH M.S.KIM,D.H.SHIN,J.LEE,K.JOO,J.PARK,D.LEE,E.A.BERRY, JRNL AUTH 2 G.-J.JHON JRNL TITL HIGH-ACCURACY PROTEIN MODELING AND ITS APPLICATION TO JRNL TITL 2 MOLECULAR REPLACEMENT OF CRYSTALLOGRAPHIC PHASING JRNL REF TO BE PUBLISHED REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1420) 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 7166 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 717 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 51.4400 - 3.9067 0.99 1531 177 0.1895 0.2462 REMARK 3 2 3.9067 - 3.1010 1.00 1539 177 0.2315 0.3149 REMARK 3 3 3.1010 - 2.7090 1.00 1518 172 0.2669 0.3725 REMARK 3 4 2.7090 - 2.4613 0.89 1393 142 0.2952 0.3776 REMARK 3 5 2.4613 - 2.2849 0.30 468 49 0.2844 0.4393 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.630 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 : 0.005 1792 REMARK 3 ANGLE : 1.274 2426 REMARK 3 CHIRALITY : 0.087 288 REMARK 3 PLANARITY : 0.005 310 REMARK 3 DIHEDRAL : 16.498 664 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 24.5925 -4.6085 0.1919 REMARK 3 T TENSOR REMARK 3 T11: 0.1726 T22: 0.1407 REMARK 3 T33: 0.2107 T12: -0.0033 REMARK 3 T13: -0.0307 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 0.8872 L22: 0.6521 REMARK 3 L33: 5.2794 L12: 0.6100 REMARK 3 L13: 2.1633 L23: 1.5285 REMARK 3 S TENSOR REMARK 3 S11: 0.0307 S12: -0.0014 S13: -0.1211 REMARK 3 S21: -0.0261 S22: -0.0109 S23: -0.0807 REMARK 3 S31: -0.1675 S32: -0.1231 S33: 0.1894 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 4TN5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000201896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.48690 REMARK 200 MONOCHROMATOR : SILICON DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7223 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 51.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: 0.1M BIS-TRIS, 10MM NICKEL (II) HLORIDE, 10MM CESIUM REMARK 200 CHLORIDE, 20% PEG MME 2000, PH 8.5, REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 10MM NICKEL (II) REMARK 280 CHLORIDE, 10MM CESIUM CHLORIDE, 20% PEG MME 2000, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.85400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.42700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 201 DBREF 4TN5 A 1 113 UNP P32676 PTFB3_ECOLI 1 113 DBREF 4TN5 B 1 113 UNP P32676 PTFB3_ECOLI 1 113 SEQRES 1 A 113 MSE ALA TYR LEU VAL ALA VAL THR ALA CYS VAL SER GLY SEQRES 2 A 113 VAL ALA HIS THR TYR MSE ALA ALA GLU ARG LEU GLU LYS SEQRES 3 A 113 LEU CYS LEU LEU GLU LYS TRP GLY VAL SER ILE GLU THR SEQRES 4 A 113 GLN GLY ALA LEU GLY THR GLU ASN ARG LEU ALA ASP GLU SEQRES 5 A 113 ASP ILE ARG ARG ALA ASP VAL ALA LEU LEU ILE THR ASP SEQRES 6 A 113 ILE GLU LEU ALA GLY ALA GLU ARG PHE GLU HIS CYS ARG SEQRES 7 A 113 TYR VAL GLN CYS SER ILE TYR ALA PHE LEU ARG GLU PRO SEQRES 8 A 113 GLN ARG VAL MSE SER ALA VAL ARG LYS VAL LEU SER ALA SEQRES 9 A 113 PRO GLN GLN THR HIS LEU ILE LEU GLU SEQRES 1 B 113 MSE ALA TYR LEU VAL ALA VAL THR ALA CYS VAL SER GLY SEQRES 2 B 113 VAL ALA HIS THR TYR MSE ALA ALA GLU ARG LEU GLU LYS SEQRES 3 B 113 LEU CYS LEU LEU GLU LYS TRP GLY VAL SER ILE GLU THR SEQRES 4 B 113 GLN GLY ALA LEU GLY THR GLU ASN ARG LEU ALA ASP GLU SEQRES 5 B 113 ASP ILE ARG ARG ALA ASP VAL ALA LEU LEU ILE THR ASP SEQRES 6 B 113 ILE GLU LEU ALA GLY ALA GLU ARG PHE GLU HIS CYS ARG SEQRES 7 B 113 TYR VAL GLN CYS SER ILE TYR ALA PHE LEU ARG GLU PRO SEQRES 8 B 113 GLN ARG VAL MSE SER ALA VAL ARG LYS VAL LEU SER ALA SEQRES 9 B 113 PRO GLN GLN THR HIS LEU ILE LEU GLU MODRES 4TN5 MSE A 1 MET MODIFIED RESIDUE MODRES 4TN5 MSE A 19 MET MODIFIED RESIDUE MODRES 4TN5 MSE A 95 MET MODIFIED RESIDUE MODRES 4TN5 MSE B 1 MET MODIFIED RESIDUE MODRES 4TN5 MSE B 19 MET MODIFIED RESIDUE MODRES 4TN5 MSE B 95 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 19 8 HET MSE A 95 8 HET MSE B 1 8 HET MSE B 19 8 HET MSE B 95 8 HET NI A 201 1 HETNAM MSE SELENOMETHIONINE HETNAM NI NICKEL (II) ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 NI NI 2+ FORMUL 4 HOH *17(H2 O) HELIX 1 AA1 THR A 17 GLU A 31 1 15 HELIX 2 AA2 ALA A 50 ALA A 57 1 8 HELIX 3 AA3 GLY A 70 GLU A 75 5 6 HELIX 4 AA4 SER A 83 GLU A 90 1 8 HELIX 5 AA5 PRO A 91 ALA A 104 1 14 HELIX 6 AA6 ALA B 15 GLU B 31 1 17 HELIX 7 AA7 ALA B 50 ALA B 57 1 8 HELIX 8 AA8 GLY B 70 GLU B 75 5 6 HELIX 9 AA9 SER B 83 GLU B 90 1 8 HELIX 10 AB1 PRO B 91 ALA B 104 1 14 SHEET 1 AA112 GLY A 44 GLU A 46 0 SHEET 2 AA112 GLY A 34 GLY A 41 -1 N THR A 39 O GLU A 46 SHEET 3 AA112 TYR A 3 ALA A 9 1 N ALA A 6 O GLU A 38 SHEET 4 AA112 VAL A 59 THR A 64 1 O LEU A 61 N VAL A 5 SHEET 5 AA112 TYR A 79 CYS A 82 1 O VAL A 80 N LEU A 62 SHEET 6 AA112 THR A 108 ILE A 111 1 O LEU A 110 N GLN A 81 SHEET 7 AA112 GLN B 107 ILE B 111 -1 O HIS B 109 N HIS A 109 SHEET 8 AA112 TYR B 79 CYS B 82 1 N TYR B 79 O LEU B 110 SHEET 9 AA112 VAL B 59 THR B 64 1 N LEU B 62 O VAL B 80 SHEET 10 AA112 TYR B 3 ALA B 9 1 N VAL B 5 O LEU B 61 SHEET 11 AA112 GLY B 34 GLY B 41 1 O GLY B 34 N LEU B 4 SHEET 12 AA112 GLY B 44 GLU B 46 -1 O GLU B 46 N THR B 39 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 LINK C TYR A 18 N MSE A 19 1555 1555 1.33 LINK C MSE A 19 N ALA A 20 1555 1555 1.33 LINK C VAL A 94 N MSE A 95 1555 1555 1.33 LINK C MSE A 95 N SER A 96 1555 1555 1.33 LINK C MSE B 1 N ALA B 2 1555 1555 1.33 LINK C TYR B 18 N MSE B 19 1555 1555 1.33 LINK C MSE B 19 N ALA B 20 1555 1555 1.33 LINK C VAL B 94 N MSE B 95 1555 1555 1.33 LINK C MSE B 95 N SER B 96 1555 1555 1.33 SITE 1 AC1 4 HIS A 109 HIS B 109 HOH B 206 HOH B 207 CRYST1 33.110 33.110 154.281 90.00 90.00 120.00 P 32 6 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 0.030202 0.017437 0.000000 0.00000 SCALE2 0.000000 0.034875 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006482 0.00000 HETATM 1 N MSE A 1 16.687 -23.514 -12.901 1.00104.46 N HETATM 2 CA MSE A 1 15.492 -23.458 -12.068 1.00106.14 C HETATM 3 C MSE A 1 15.544 -22.254 -11.134 1.00 94.98 C HETATM 4 O MSE A 1 14.608 -22.004 -10.374 1.00 96.65 O HETATM 5 CB MSE A 1 15.341 -24.749 -11.262 1.00116.86 C HETATM 6 CG MSE A 1 16.399 -24.936 -10.188 1.00119.64 C HETATM 7 SE MSE A 1 16.427 -26.744 -9.460 1.00111.62 SE HETATM 8 CE MSE A 1 17.613 -27.571 -10.769 1.00107.13 C