HEADER TRANSFERASE 28-MAR-13 4JXD OBSLTE 10-JUN-15 4JXD 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: PREDICTED FRUCTOSE SPECIFIC IIB, PTS SYSTEM FRUCTOSE-LIKE COMPND 5 EIIB COMPONENT 3; COMPND 6 EC: 2.7.1.69; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: FRWD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IIB, EIIB(FRUC), ALPHA/BETA, PHOSPHORYL GROUP TRANSFERASE, EIIA, KEYWDS 2 EIIC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.H.SHIN,M.S.KIM REVDAT 2 10-JUN-15 4JXD 1 OBSLTE REVDAT 1 07-MAY-14 4JXD 0 JRNL AUTH D.H.SHIN,M.S.KIM JRNL TITL CRYSTAL STRUCTURE OF PREDICTED FRUCTOSE SPECIFIC IIB FROM JRNL TITL 2 ESCHERICHIA COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 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- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 7005 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 323 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 28.6761 - 3.0249 1.00 3505 160 0.2352 0.2924 REMARK 3 2 3.0249 - 2.4013 0.90 3177 163 0.2615 0.3556 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) : 38.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.20 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: 0.4900 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1792 REMARK 3 ANGLE : 1.541 2426 REMARK 3 CHIRALITY : 0.103 288 REMARK 3 PLANARITY : 0.023 310 REMARK 3 DIHEDRAL : 16.757 664 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 4JXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-APR-13. REMARK 100 THE RCSB ID CODE IS RCSB078623. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 51.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.25 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 102.85333 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 51.42667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 VAL A 14 -4.10 -140.21 REMARK 500 VAL B 14 -14.45 -140.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 23 0.29 SIDE CHAIN REMARK 500 ARG B 23 0.23 SIDE CHAIN 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 NI A 201 DBREF 4JXD A 1 113 UNP P32676 PTFB3_ECOLI 1 113 DBREF 4JXD 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 4JXD MSE A 1 MET SELENOMETHIONINE MODRES 4JXD MSE A 19 MET SELENOMETHIONINE MODRES 4JXD MSE A 95 MET SELENOMETHIONINE MODRES 4JXD MSE B 1 MET SELENOMETHIONINE MODRES 4JXD MSE B 19 MET SELENOMETHIONINE MODRES 4JXD MSE B 95 MET SELENOMETHIONINE 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 *15(H2 O) HELIX 1 1 VAL A 14 GLU A 31 1 18 HELIX 2 2 ALA A 50 ARG A 55 1 6 HELIX 3 3 GLY A 70 GLU A 75 5 6 HELIX 4 4 SER A 83 GLU A 90 1 8 HELIX 5 5 GLU A 90 ALA A 104 1 15 HELIX 6 6 VAL B 14 GLU B 31 1 18 HELIX 7 7 ALA B 50 ARG B 55 1 6 HELIX 8 8 GLY B 70 GLU B 75 5 6 HELIX 9 9 SER B 83 GLU B 90 1 8 HELIX 10 10 GLU B 90 ALA B 104 1 15 SHEET 1 A12 GLY A 44 GLU A 46 0 SHEET 2 A12 GLY A 34 GLY A 41 -1 N THR A 39 O GLU A 46 SHEET 3 A12 TYR A 3 ALA A 9 1 N ALA A 6 O GLU A 38 SHEET 4 A12 VAL A 59 THR A 64 1 O ILE A 63 N VAL A 7 SHEET 5 A12 TYR A 79 CYS A 82 1 O CYS A 82 N THR A 64 SHEET 6 A12 GLN A 107 ILE A 111 1 O LEU A 110 N TYR A 79 SHEET 7 A12 HIS B 109 ILE B 111 -1 O HIS B 109 N HIS A 109 SHEET 8 A12 TYR B 79 CYS B 82 1 N GLN B 81 O LEU B 110 SHEET 9 A12 VAL B 59 THR B 64 1 N THR B 64 O CYS B 82 SHEET 10 A12 TYR B 3 ALA B 9 1 N VAL B 7 O ILE B 63 SHEET 11 A12 GLY B 34 GLY B 41 1 O GLU B 38 N ALA B 6 SHEET 12 A12 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 1.30 LINK C MSE A 19 N ALA A 20 1555 1555 1.31 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 1.31 LINK C MSE B 19 N ALA B 20 1555 1555 1.31 LINK C VAL B 94 N MSE B 95 1555 1555 1.32 LINK C MSE B 95 N SER B 96 1555 1555 1.32 SITE 1 AC1 3 HIS A 109 HIS B 109 HOH B 201 CRYST1 33.110 33.110 154.280 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 27.339 17.667 90.379 1.00 84.49 N HETATM 2 CA MSE A 1 28.192 16.768 91.146 1.00 86.66 C HETATM 3 C MSE A 1 27.375 15.791 91.978 1.00 77.43 C HETATM 4 O MSE A 1 27.838 14.704 92.310 1.00 79.18 O HETATM 5 CB MSE A 1 29.144 17.562 92.042 1.00100.15 C HETATM 6 CG MSE A 1 30.270 16.724 92.612 1.00111.16 C HETATM 7 SE MSE A 1 30.788 15.298 91.377 1.00199.43 SE HETATM 8 CE MSE A 1 31.461 16.349 89.867 1.00106.52 C