Header list of 1y6d.pdb file
Complete list - r 2 2 Bytes
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
Complete list - r 2 2 Bytes