10 20 30 40 50 60 70 80 2I2H - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN 16-AUG-06 2I2H
TITLE NMR STRUCTURE OF TPC3 IN TFE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNALING PEPTIDE TCP3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COMPETENCE STIMULATING PEPTIDE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: MUTATED ORGANISM, THE SEQUENCE OF THIS SOURCE 4 PEPTIDE CAN BE FOUND IN STREPTOCOCCUS MUTANTS JH1005
KEYWDS HELIX, SIGNALING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 22
AUTHOR R.T.SYVITSKI,D.L.JAKEMAN,Y.LI
REVDAT 3 24-FEB-09 2I2H 1 VERSN REVDAT 2 13-FEB-07 2I2H 1 JRNL REVDAT 1 17-OCT-06 2I2H 0
JRNL AUTH R.T.SYVITSKI,X.L.TIAN,K.SAMPARA,A.SALMAN,S.F.LEE, JRNL AUTH 2 D.L.JAKEMAN,Y.H.LI JRNL TITL STRUCTURE-ACTIVITY ANALYSIS OF QUORUM-SENSING JRNL TITL 2 SIGNALING PEPTIDES FROM STREPTOCOCCUS MUTANS. JRNL REF J.BACTERIOL. V. 189 1441 2007 JRNL REFN ISSN 0021-9193 JRNL PMID 16936029 JRNL DOI 10.1128/JB.00832-06
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER A.T. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2I2H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB039053.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM PEPTIDE, 100% TFE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 150MS TOCSY, 250MS NOESY, DOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, SPARKY 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 22 REMARK 210 CONFORMERS, SELECTION CRITERIA : NON-VIOLATING STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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 THR A 3 N SER A 5 2.11 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 1 SER A 1 N SER A 1 CA -1.297 REMARK 500 1 SER A 1 CA SER A 1 CB -1.077 REMARK 500 1 SER A 1 CB SER A 1 OG -1.191 REMARK 500 1 SER A 1 CA SER A 1 C -0.987 REMARK 500 1 SER A 1 C SER A 1 O -1.056 REMARK 500 1 GLY A 2 N GLY A 2 CA -0.921 REMARK 500 1 GLY A 2 CA GLY A 2 C -0.577 REMARK 500 1 GLY A 2 C GLY A 2 O -0.710 REMARK 500 1 SER A 1 C GLY A 2 N -0.891 REMARK 500 1 THR A 3 N THR A 3 CA -0.542 REMARK 500 1 THR A 3 CA THR A 3 CB -0.588 REMARK 500 1 THR A 3 CB THR A 3 OG1 -0.530 REMARK 500 1 THR A 3 CB THR A 3 CG2 -0.886 REMARK 500 1 THR A 3 C THR A 3 O -0.287 REMARK 500 1 GLY A 2 C THR A 3 N -0.704 REMARK 500 1 LEU A 4 CB LEU A 4 CG -0.398 REMARK 500 1 LEU A 4 CG LEU A 4 CD1 -0.680 REMARK 500 1 LEU A 4 CG LEU A 4 CD2 -0.670 REMARK 500 1 THR A 3 C LEU A 4 N -0.814 REMARK 500 1 SER A 5 CB SER A 5 OG -0.573 REMARK 500 1 PHE A 7 CG PHE A 7 CD2 -0.248 REMARK 500 1 PHE A 7 CG PHE A 7 CD1 -0.242 REMARK 500 1 PHE A 7 CE1 PHE A 7 CZ -0.234 REMARK 500 1 PHE A 7 CZ PHE A 7 CE2 -0.228 REMARK 500 1 PHE A 8 CB PHE A 8 CG -0.218 REMARK 500 1 PHE A 8 CG PHE A 8 CD2 -0.558 REMARK 500 1 PHE A 8 CG PHE A 8 CD1 -0.385 REMARK 500 1 PHE A 8 CD1 PHE A 8 CE1 -0.190 REMARK 500 1 PHE A 8 CE1 PHE A 8 CZ -0.544 REMARK 500 1 PHE A 8 CZ PHE A 8 CE2 -0.372 REMARK 500 1 PHE A 8 CE2 PHE A 8 CD2 -0.191 REMARK 500 1 ARG A 9 CB ARG A 9 CG -0.243 REMARK 500 1 ARG A 9 CG ARG A 9 CD -0.563 REMARK 500 1 ARG A 9 CD ARG A 9 NE -0.738 REMARK 500 1 ARG A 9 NE ARG A 9 CZ -0.656 REMARK 500 1 ARG A 9 CZ ARG A 9 NH1 -0.727 REMARK 500 1 ARG A 9 CZ ARG A 9 NH2 -0.591 REMARK 500 1 LEU A 10 CG LEU A 10 CD1 -0.669 REMARK 500 1 LEU A 10 CG LEU A 10 CD2 -0.744 REMARK 500 1 PHE A 11 CB PHE A 11 CG -0.137 REMARK 500 1 PHE A 11 CG PHE A 11 CD2 -0.250 REMARK 500 1 PHE A 11 CG PHE A 11 CD1 -0.281 REMARK 500 1 PHE A 11 CE1 PHE A 11 CZ -0.236 REMARK 500 1 PHE A 11 CZ PHE A 11 CE2 -0.267 REMARK 500 1 ASN A 12 CG ASN A 12 OD1 -0.678 REMARK 500 1 ASN A 12 CG ASN A 12 ND2 -0.533 REMARK 500 1 ARG A 13 CB ARG A 13 CG -0.259 REMARK 500 1 ARG A 13 CG ARG A 13 CD -0.619 REMARK 500 1 ARG A 13 CD ARG A 13 NE -0.767 REMARK 500 1 ARG A 13 NE ARG A 13 CZ -0.587 REMARK 500 REMARK 500 THIS ENTRY HAS 74 BOND DEVIATIONS. 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 1 SER A 1 CB - CA - C ANGL. DEV. = 41.7 DEGREES REMARK 500 1 SER A 1 N - CA - CB ANGL. DEV. = -53.2 DEGREES REMARK 500 1 SER A 1 CA - CB - OG ANGL. DEV. = 40.5 DEGREES REMARK 500 1 SER A 1 N - CA - C ANGL. DEV. = 25.6 DEGREES REMARK 500 1 SER A 1 CA - C - O ANGL. DEV. = -13.6 DEGREES REMARK 500 1 GLY A 2 N - CA - C ANGL. DEV. = 27.9 DEGREES REMARK 500 1 SER A 1 CA - C - N ANGL. DEV. = 39.5 DEGREES REMARK 500 1 SER A 1 O - C - N ANGL. DEV. = -25.4 DEGREES REMARK 500 1 GLY A 2 C - N - CA ANGL. DEV. = 34.5 DEGREES REMARK 500 1 THR A 3 CB - CA - C ANGL. DEV. = 24.2 DEGREES REMARK 500 1 THR A 3 N - CA - CB ANGL. DEV. = -38.3 DEGREES REMARK 500 1 THR A 3 OG1 - CB - CG2 ANGL. DEV. = -44.5 DEGREES REMARK 500 1 THR A 3 CA - CB - OG1 ANGL. DEV. = 27.3 DEGREES REMARK 500 1 THR A 3 CA - CB - CG2 ANGL. DEV. = 10.8 DEGREES REMARK 500 1 THR A 3 N - CA - C ANGL. DEV. = 23.8 DEGREES REMARK 500 1 THR A 3 CA - C - O ANGL. DEV. = 35.4 DEGREES REMARK 500 1 GLY A 2 CA - C - N ANGL. DEV. = 16.6 DEGREES REMARK 500 1 GLY A 2 O - C - N ANGL. DEV. = -25.1 DEGREES REMARK 500 1 LEU A 4 CD1 - CG - CD2 ANGL. DEV. = -32.7 DEGREES REMARK 500 1 LEU A 4 CB - CG - CD1 ANGL. DEV. = 19.8 DEGREES REMARK 500 1 LEU A 4 CB - CG - CD2 ANGL. DEV. = 12.0 DEGREES REMARK 500 1 THR A 3 O - C - N ANGL. DEV. = -41.9 DEGREES REMARK 500 1 PHE A 7 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 PHE A 7 CD1 - CG - CD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 PHE A 7 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 PHE A 8 CD1 - CG - CD2 ANGL. DEV. = -19.8 DEGREES REMARK 500 1 PHE A 8 CB - CG - CD1 ANGL. DEV. = 16.3 DEGREES REMARK 500 1 PHE A 8 CG - CD1 - CE1 ANGL. DEV. = 16.2 DEGREES REMARK 500 1 PHE A 8 CE1 - CZ - CE2 ANGL. DEV. = -21.6 DEGREES REMARK 500 1 PHE A 8 CZ - CE2 - CD2 ANGL. DEV. = 17.0 DEGREES REMARK 500 1 ARG A 9 CB - CG - CD ANGL. DEV. = 26.7 DEGREES REMARK 500 1 ARG A 9 CG - CD - NE ANGL. DEV. = 53.0 DEGREES REMARK 500 1 ARG A 9 CD - NE - CZ ANGL. DEV. = 51.9 DEGREES REMARK 500 1 ARG A 9 NE - CZ - NH1 ANGL. DEV. = -10.9 DEGREES REMARK 500 1 ARG A 9 NE - CZ - NH2 ANGL. DEV. = 9.6 DEGREES REMARK 500 1 LEU A 10 CD1 - CG - CD2 ANGL. DEV. = -29.4 DEGREES REMARK 500 1 LEU A 10 CB - CG - CD1 ANGL. DEV. = 22.4 DEGREES REMARK 500 1 LEU A 10 CB - CG - CD2 ANGL. DEV. = 13.4 DEGREES REMARK 500 1 PHE A 11 CB - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 ASN A 12 OD1 - CG - ND2 ANGL. DEV. = -59.6 DEGREES REMARK 500 1 ASN A 12 CB - CG - OD1 ANGL. DEV. = 22.6 DEGREES REMARK 500 1 ASN A 12 CB - CG - ND2 ANGL. DEV. = 36.8 DEGREES REMARK 500 1 ARG A 13 CB - CG - CD ANGL. DEV. = 27.4 DEGREES REMARK 500 1 ARG A 13 CG - CD - NE ANGL. DEV. = 38.3 DEGREES REMARK 500 1 ARG A 13 CD - NE - CZ ANGL. DEV. = 45.0 DEGREES REMARK 500 1 ARG A 13 NH1 - CZ - NH2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 21.9 DEGREES REMARK 500 1 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -11.6 DEGREES REMARK 500 1 SER A 14 CA - CB - OG ANGL. DEV. = 24.9 DEGREES REMARK 500 1 PHE A 15 CB - CG - CD2 ANGL. DEV. = 8.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 64 ANGLE DEVIATIONS. 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 LEU A 4 -34.24 -33.20 REMARK 500 2 THR A 3 -51.54 -130.02 REMARK 500 2 SER A 5 -70.33 -59.63 REMARK 500 2 GLN A 17 -72.24 -105.47 REMARK 500 3 THR A 3 -70.37 -121.11 REMARK 500 3 GLN A 17 -73.03 -76.73 REMARK 500 5 THR A 3 -81.22 -138.16 REMARK 500 5 GLN A 17 -82.82 -83.27 REMARK 500 6 LEU A 4 -0.52 71.85 REMARK 500 7 THR A 16 -81.92 -57.56 REMARK 500 8 GLN A 17 -73.46 -147.10 REMARK 500 11 THR A 3 -57.95 -159.15 REMARK 500 11 LEU A 4 -0.13 71.68 REMARK 500 13 THR A 3 -87.20 -96.09 REMARK 500 13 LEU A 4 -0.29 71.55 REMARK 500 14 THR A 3 -61.76 -162.54 REMARK 500 14 LEU A 4 -0.44 71.65 REMARK 500 15 LEU A 4 -0.89 71.89 REMARK 500 15 SER A 5 -70.06 -59.33 REMARK 500 15 GLN A 17 -85.47 -47.71 REMARK 500 16 GLN A 17 -74.44 -131.79 REMARK 500 17 THR A 3 -51.40 -130.64 REMARK 500 18 THR A 3 -77.80 -120.37 REMARK 500 19 LEU A 4 -0.28 71.56 REMARK 500 19 GLN A 17 -74.56 -75.13 REMARK 500 20 THR A 3 -80.46 -157.59 REMARK 500 21 THR A 3 -80.50 -144.86 REMARK 500 21 LEU A 4 -0.00 71.47 REMARK 500 22 THR A 3 -64.71 -130.12 REMARK 500 22 GLN A 17 -69.24 -109.04 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 2 ARG A 9 0.27 SIDE_CHAIN REMARK 500 2 ARG A 13 0.27 SIDE_CHAIN REMARK 500 3 ARG A 9 0.31 SIDE_CHAIN REMARK 500 3 ARG A 13 0.18 SIDE_CHAIN REMARK 500 4 ARG A 9 0.25 SIDE_CHAIN REMARK 500 4 ARG A 13 0.30 SIDE_CHAIN REMARK 500 5 ARG A 9 0.27 SIDE_CHAIN REMARK 500 5 ARG A 13 0.22 SIDE_CHAIN REMARK 500 6 ARG A 9 0.29 SIDE_CHAIN REMARK 500 6 ARG A 13 0.11 SIDE_CHAIN REMARK 500 7 ARG A 9 0.27 SIDE_CHAIN REMARK 500 7 ARG A 13 0.09 SIDE_CHAIN REMARK 500 8 ARG A 9 0.19 SIDE_CHAIN REMARK 500 8 ARG A 13 0.20 SIDE_CHAIN REMARK 500 9 ARG A 9 0.26 SIDE_CHAIN REMARK 500 9 ARG A 13 0.24 SIDE_CHAIN REMARK 500 10 ARG A 9 0.29 SIDE_CHAIN REMARK 500 10 ARG A 13 0.15 SIDE_CHAIN REMARK 500 11 ARG A 9 0.18 SIDE_CHAIN REMARK 500 11 ARG A 13 0.28 SIDE_CHAIN REMARK 500 12 ARG A 9 0.27 SIDE_CHAIN REMARK 500 12 ARG A 13 0.30 SIDE_CHAIN REMARK 500 13 ARG A 9 0.11 SIDE_CHAIN REMARK 500 13 ARG A 13 0.21 SIDE_CHAIN REMARK 500 14 ARG A 9 0.30 SIDE_CHAIN REMARK 500 14 ARG A 13 0.28 SIDE_CHAIN REMARK 500 15 ARG A 9 0.17 SIDE_CHAIN REMARK 500 15 ARG A 13 0.31 SIDE_CHAIN REMARK 500 16 ARG A 9 0.15 SIDE_CHAIN REMARK 500 16 ARG A 13 0.19 SIDE_CHAIN REMARK 500 17 ARG A 9 0.09 SIDE_CHAIN REMARK 500 17 ARG A 13 0.29 SIDE_CHAIN REMARK 500 18 ARG A 9 0.31 SIDE_CHAIN REMARK 500 18 ARG A 13 0.17 SIDE_CHAIN REMARK 500 19 ARG A 9 0.29 SIDE_CHAIN REMARK 500 19 ARG A 13 0.21 SIDE_CHAIN REMARK 500 20 ARG A 9 0.31 SIDE_CHAIN REMARK 500 20 ARG A 13 0.19 SIDE_CHAIN REMARK 500 21 ARG A 9 0.24 SIDE_CHAIN REMARK 500 21 ARG A 13 0.27 SIDE_CHAIN REMARK 500 22 ARG A 9 0.31 SIDE_CHAIN REMARK 500 22 ARG A 13 0.31 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 2I2H A 1 19 PDB 2I2H 2I2H 1 19
SEQRES 1 A 19 SER GLY THR LEU SER THR PHE PHE ARG LEU PHE ASN ARG SEQRES 2 A 19 SER PHE THR GLN ALA NH2
HET NH2 A 19 3
HETNAM NH2 AMINO GROUP
FORMUL 1 NH2 H2 N
HELIX 1 1 LEU A 4 ALA A 18 1 15
LINK N ALA A 18 N NH2 A 19 1555 1555 1.60
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