HEADER TRANSFERASE 06-DEC-04 1Y6D TITLE SOLUTION STRUCTURE AND DYNAMICS OF LUXU FROM VIBRIO HARVEYI, A TITLE 2 PHOSPHOTRANSFERASE PROTEIN INVOLVED IN BACTERIAL QUORUM SENSING COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORELAY PROTEIN LUXU; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO HARVEYI; SOURCE 3 ORGANISM_TAXID: 669; SOURCE 4 GENE: LUXU; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3 PLYS-S; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDLU KEYWDS PHOSPHOTRANSFERASE, FOUR-HELIX BUNDLE, QUORUM SENSING, PHOSPHORELAY, KEYWDS 2 TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR D.L.ULRICH,D.KOJETIN,B.L.BASSLER,J.CAVANAGH,J.P.LORIA REVDAT 5 02-MAR-22 1Y6D 1 REMARK SEQADV REVDAT 4 24-FEB-09 1Y6D 1 VERSN REVDAT 3 12-APR-05 1Y6D 1 JRNL REVDAT 2 04-JAN-05 1Y6D 1 SEQRES SEQADV REVDAT 1 14-DEC-04 1Y6D 0 JRNL AUTH D.L.ULRICH,D.KOJETIN,B.L.BASSLER,J.CAVANAGH,J.P.LORIA JRNL TITL SOLUTION STRUCTURE AND DYNAMICS OF LUXU FROM VIBRIO HARVEYI, JRNL TITL 2 A PHOSPHOTRANSFERASE PROTEIN INVOLVED IN BACTERIAL QUORUM JRNL TITL 3 SENSING. JRNL REF J.MOL.BIOL. V. 347 297 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15740742 JRNL DOI 10.1016/J.JMB.2005.01.039 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.L.ULRICH,R.THOMPSON,B.BASSLER,J.CAVANAGH,J.P.LORIA REMARK 1 TITL 1H,15N,AND 13C CHEMICAL SHIFT ASSIGNMENTS OF THE VIBRIO REMARK 1 TITL 2 HARVEYI HISTIDINE PHOSPHOTRANSFERASE PROTEIN LUXU REMARK 1 REF J.BIOMOL.NMR V. 29 551 2004 REMARK 1 REFN ISSN 0925-2738 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : C.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJANDRA,G.M.CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y6D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031172. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 294; 294 REMARK 210 PH : 6.4; 6.4 REMARK 210 IONIC STRENGTH : 300MM NACL; 300MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM LUXU U-15N, 50MM PHOSPHATE REMARK 210 BUFFER, 300MM NACL, 90% H2O, 10% REMARK 210 D2O; 1MM LUXU U-15N,13C, 50MM REMARK 210 PHOSPHATE BUFFER, 300MM NACL, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA; 3D_13C- REMARK 210 SEPARATED_NOESY; 3D 13C HCCH- REMARK 210 TOCSY; HNCA; HNCOCA; HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CNS 1.0, SPARKY, DYANA REMARK 210 CYANA, TALOS REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 19 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 17 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-19 REMARK 465 RES C SSSEQI REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS A 54 H HIS A 58 1.55 REMARK 500 O LEU A 51 HZ1 LYS A 54 1.58 REMARK 500 O SER A 63 H PHE A 67 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 4 GLY A 19 N GLY A 19 CA -0.092 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 TYR A 37 CA - CB - CG ANGL. DEV. = -11.4 DEGREES REMARK 500 2 TYR A 37 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 4 TYR A 37 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 TYR A 37 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 11 TYR A 37 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 12 TYR A 37 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 18 TYR A 37 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 ASP A 4 81.04 -67.72 REMARK 500 1 VAL A 5 -39.06 -179.63 REMARK 500 1 GLN A 9 -75.83 -77.20 REMARK 500 1 SER A 15 -101.40 -57.11 REMARK 500 1 ALA A 16 -134.65 49.44 REMARK 500 1 ILE A 18 -99.36 -106.50 REMARK 500 1 GLN A 45 -167.42 -170.07 REMARK 500 1 GLU A 48 -41.27 -27.70 REMARK 500 1 LEU A 51 -34.44 -39.03 REMARK 500 1 HIS A 58 -83.37 -66.46 REMARK 500 1 ALA A 69 24.94 -71.49 REMARK 500 1 ASP A 70 -132.70 -121.61 REMARK 500 1 ASP A 80 -60.21 -100.97 REMARK 500 1 ALA A 83 -34.92 -136.98 REMARK 500 1 MET A 93 32.02 34.27 REMARK 500 1 THR A 95 -63.02 176.02 REMARK 500 1 TRP A 112 7.88 -155.03 REMARK 500 1 THR A 113 34.20 -141.68 REMARK 500 2 ASP A 4 79.29 -68.66 REMARK 500 2 VAL A 5 -36.44 -176.69 REMARK 500 2 SER A 15 -85.19 -65.47 REMARK 500 2 ALA A 16 -139.24 46.90 REMARK 500 2 ILE A 18 -85.46 -108.65 REMARK 500 2 SER A 20 15.28 -68.77 REMARK 500 2 ASP A 21 -42.67 -150.05 REMARK 500 2 GLN A 45 -154.90 -175.68 REMARK 500 2 GLU A 48 -44.09 -29.13 REMARK 500 2 HIS A 58 -79.05 -76.50 REMARK 500 2 ALA A 69 23.79 -72.41 REMARK 500 2 ASP A 70 -126.15 -117.22 REMARK 500 2 ASP A 80 -66.53 -97.16 REMARK 500 2 ALA A 83 -36.84 -138.84 REMARK 500 2 LEU A 88 -84.76 -63.75 REMARK 500 2 MET A 93 79.20 39.18 REMARK 500 2 GLU A 94 12.53 -145.86 REMARK 500 2 THR A 95 -55.51 170.13 REMARK 500 2 THR A 113 -68.32 -126.35 REMARK 500 3 THR A 3 156.95 135.48 REMARK 500 3 VAL A 5 -36.69 177.39 REMARK 500 3 SER A 15 -85.98 -66.13 REMARK 500 3 ALA A 16 -133.82 50.00 REMARK 500 3 ILE A 18 -96.32 -110.52 REMARK 500 3 SER A 47 -70.35 -41.10 REMARK 500 3 GLU A 48 -42.83 -27.06 REMARK 500 3 HIS A 58 -79.62 160.27 REMARK 500 3 ALA A 69 37.22 -81.90 REMARK 500 3 ASP A 70 -89.07 -119.68 REMARK 500 3 ILE A 77 -76.24 -41.93 REMARK 500 3 ASP A 80 -71.86 -94.07 REMARK 500 3 ALA A 83 -42.58 -141.78 REMARK 500 REMARK 500 THIS ENTRY HAS 347 RAMACHANDRAN OUTLIERS. 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 1 ARG A 110 0.08 SIDE CHAIN REMARK 500 4 ARG A 110 0.10 SIDE CHAIN REMARK 500 12 ARG A 75 0.07 SIDE CHAIN REMARK 500 15 ARG A 110 0.11 SIDE CHAIN REMARK 500 16 ARG A 75 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 ILE A 79 -13.11 REMARK 500 1 LYS A 81 -11.04 REMARK 500 2 ILE A 79 -11.37 REMARK 500 3 ILE A 79 -10.25 REMARK 500 4 ILE A 79 -11.64 REMARK 500 5 ILE A 79 -10.71 REMARK 500 6 ILE A 79 -12.89 REMARK 500 10 ILE A 79 -10.60 REMARK 500 12 ILE A 79 -15.06 REMARK 500 12 LYS A 81 -11.98 REMARK 500 12 LYS A 82 -10.62 REMARK 500 14 ILE A 79 -11.47 REMARK 500 14 LYS A 81 -10.34 REMARK 500 15 ILE A 79 -13.21 REMARK 500 16 ILE A 79 -12.29 REMARK 500 19 ILE A 79 -11.26 REMARK 500 REMARK 500 REMARK: NULL DBREF 1Y6D A 1 114 UNP Q9ZBB6 LUXU_VIBHA 1 114 SEQADV 1Y6D HIS A -5 UNP Q9ZBB6 EXPRESSION TAG SEQADV 1Y6D HIS A -4 UNP Q9ZBB6 EXPRESSION TAG SEQADV 1Y6D HIS A -3 UNP Q9ZBB6 EXPRESSION TAG SEQADV 1Y6D HIS A -2 UNP Q9ZBB6 EXPRESSION TAG SEQADV 1Y6D HIS A -1 UNP Q9ZBB6 EXPRESSION TAG SEQADV 1Y6D HIS A 0 UNP Q9ZBB6 EXPRESSION TAG SEQRES 1 A 120 HIS HIS HIS HIS HIS HIS MET ASN THR ASP VAL LEU ASN SEQRES 2 A 120 GLN GLN LYS ILE GLU GLU LEU SER ALA GLU ILE GLY SER SEQRES 3 A 120 ASP ASN VAL PRO VAL LEU LEU ASP ILE PHE LEU GLY GLU SEQRES 4 A 120 MET ASP SER TYR ILE GLY THR LEU THR GLU LEU GLN GLY SEQRES 5 A 120 SER GLU GLN LEU LEU TYR LEU LYS GLU ILE SER HIS ALA SEQRES 6 A 120 LEU LYS SER SER ALA ALA SER PHE GLY ALA ASP ARG LEU SEQRES 7 A 120 CYS GLU ARG ALA ILE ALA ILE ASP LYS LYS ALA LYS ALA SEQRES 8 A 120 ASN GLN LEU GLN GLU GLN GLY MET GLU THR SER GLU MET SEQRES 9 A 120 LEU ALA LEU LEU HIS ILE THR ARG ASP ALA TYR ARG SER SEQRES 10 A 120 TRP THR ASN HELIX 1 1 GLN A 9 SER A 15 1 7 HELIX 2 2 SER A 15 LEU A 41 1 27 HELIX 3 3 GLY A 46 HIS A 58 1 13 HELIX 4 4 HIS A 58 GLY A 68 1 11 HELIX 5 5 ASP A 70 ALA A 83 1 14 HELIX 6 6 ALA A 83 GLN A 89 1 7 HELIX 7 7 LEU A 99 THR A 113 1 15 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1