HEADER SIGNALING PROTEIN 12-MAR-18 6COT TITLE CSP2-D10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPETENCE-STIMULATING PEPTIDE TYPE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-41; COMPND 5 SYNONYM: CSP-2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 4 ORGANISM_TAXID: 1313 KEYWDS PNEUMOCOCCUS, QUORUM SENSING, SIGNALING MOLECULE, CSP, SIGNALING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.YANG REVDAT 3 19-SEP-18 6COT 1 JRNL REVDAT 2 05-SEP-18 6COT 1 JRNL REVDAT 1 29-AUG-18 6COT 0 JRNL AUTH Y.YANG,G.CORNILESCU,Y.TAL-GAN JRNL TITL STRUCTURAL CHARACTERIZATION OF COMPETENCE-STIMULATING JRNL TITL 2 PEPTIDE ANALOGUES REVEALS KEY FEATURES FOR COMD1 AND COMD2 JRNL TITL 3 RECEPTOR BINDING IN STREPTOCOCCUS PNEUMONIAE. JRNL REF BIOCHEMISTRY V. 57 5359 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 30125091 JRNL DOI 10.1021/ACS.BIOCHEM.8B00653 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ALSO TORSION ANGLE DYNAMICS WITH EEFX REMARK 3 REFINEMENT REMARK 4 REMARK 4 6COT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233134. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 250 MM D DPC, 1.9 MM COMPETENCE REMARK 210 STIMULATING PEPTIDE TYPE 2 REMARK 210 MUTANT-CSP2D10, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H COSY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 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 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 ILE A 8 N ILE A 8 CA -0.122 REMARK 500 1 PHE A 13 CB PHE A 13 CG -0.127 REMARK 500 2 PHE A 13 CB PHE A 13 CG -0.125 REMARK 500 3 ILE A 8 N ILE A 8 CA -0.120 REMARK 500 3 PHE A 13 CB PHE A 13 CG -0.126 REMARK 500 4 PHE A 13 CB PHE A 13 CG -0.123 REMARK 500 5 PHE A 13 CB PHE A 13 CG -0.132 REMARK 500 6 ILE A 8 N ILE A 8 CA -0.143 REMARK 500 6 PHE A 13 CB PHE A 13 CG -0.128 REMARK 500 7 PHE A 13 CB PHE A 13 CG -0.129 REMARK 500 8 PHE A 13 CB PHE A 13 CG -0.125 REMARK 500 9 PHE A 13 CB PHE A 13 CG -0.124 REMARK 500 10 PHE A 13 CB PHE A 13 CG -0.126 REMARK 500 11 PHE A 13 CB PHE A 13 CG -0.122 REMARK 500 12 PHE A 13 CB PHE A 13 CG -0.127 REMARK 500 13 PHE A 13 CB PHE A 13 CG -0.123 REMARK 500 14 ILE A 8 N ILE A 8 CA -0.121 REMARK 500 14 PHE A 13 CB PHE A 13 CG -0.124 REMARK 500 15 PHE A 13 CB PHE A 13 CG -0.126 REMARK 500 16 PHE A 13 CB PHE A 13 CG -0.133 REMARK 500 17 ILE A 8 N ILE A 8 CA -0.121 REMARK 500 17 PHE A 13 CB PHE A 13 CG -0.128 REMARK 500 18 PHE A 13 CB PHE A 13 CG -0.128 REMARK 500 19 ILE A 8 N ILE A 8 CA -0.143 REMARK 500 19 PHE A 13 CB PHE A 13 CG -0.126 REMARK 500 20 PHE A 13 CB PHE A 13 CG -0.122 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 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 3 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 4 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 5 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 6 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 7 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 8 PHE A 13 CB - CG - CD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 9 PHE A 13 CB - CG - CD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 10 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 11 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 12 PHE A 13 CB - CG - CD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 13 PHE A 13 CB - CG - CD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 14 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 15 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 16 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 17 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 18 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 19 PHE A 11 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 19 PHE A 13 CB - CG - CD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 20 PHE A 13 CB - CG - CD1 ANGL. DEV. = -5.7 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 SER A 5 29.56 -159.74 REMARK 500 1 ARG A 6 -27.80 -160.03 REMARK 500 1 LEU A 9 -37.87 -151.47 REMARK 500 1 DAS A 10 6.38 -74.37 REMARK 500 1 LEU A 12 -61.73 -90.86 REMARK 500 2 SER A 5 37.45 -174.08 REMARK 500 2 ARG A 6 -40.61 -149.49 REMARK 500 2 LEU A 9 -39.86 -148.77 REMARK 500 2 DAS A 10 4.26 -74.29 REMARK 500 3 ILE A 4 24.25 -142.84 REMARK 500 3 SER A 5 28.25 -160.26 REMARK 500 3 ARG A 6 -27.84 -158.97 REMARK 500 3 LEU A 9 -38.03 -151.54 REMARK 500 3 DAS A 10 6.14 -74.27 REMARK 500 3 LEU A 12 -61.00 -90.57 REMARK 500 4 ILE A 4 24.45 -150.03 REMARK 500 4 SER A 5 35.76 -167.08 REMARK 500 4 ARG A 6 -32.79 -170.73 REMARK 500 4 LEU A 9 -38.09 -148.45 REMARK 500 4 DAS A 10 7.75 -74.65 REMARK 500 4 LEU A 12 -61.28 -90.87 REMARK 500 5 ILE A 4 23.80 -149.34 REMARK 500 5 SER A 5 31.91 -169.06 REMARK 500 5 ARG A 6 -34.78 -156.12 REMARK 500 5 LEU A 9 -42.43 -150.32 REMARK 500 5 LEU A 12 -65.62 -105.25 REMARK 500 5 LEU A 14 31.30 -80.95 REMARK 500 5 ARG A 15 -53.63 -156.15 REMARK 500 6 ILE A 4 23.91 -144.90 REMARK 500 6 SER A 5 34.81 -163.71 REMARK 500 6 ARG A 6 -30.51 -167.36 REMARK 500 6 LEU A 9 -39.72 -151.59 REMARK 500 6 DAS A 10 7.91 -74.82 REMARK 500 6 LEU A 12 -60.50 -90.66 REMARK 500 7 ILE A 4 24.03 -151.56 REMARK 500 7 SER A 5 38.34 -168.96 REMARK 500 7 ARG A 6 -31.78 -174.34 REMARK 500 7 LEU A 9 -38.01 -148.60 REMARK 500 7 DAS A 10 7.53 -74.49 REMARK 500 7 LEU A 12 -61.24 -91.11 REMARK 500 8 ARG A 3 44.55 -109.34 REMARK 500 8 ILE A 4 25.44 -154.71 REMARK 500 8 SER A 5 37.28 -166.64 REMARK 500 8 ARG A 6 -30.35 -176.07 REMARK 500 8 LEU A 9 -38.21 -147.52 REMARK 500 8 DAS A 10 7.05 -73.91 REMARK 500 8 PHE A 11 12.00 -141.52 REMARK 500 8 LEU A 12 -60.73 -100.85 REMARK 500 8 LEU A 14 3.44 -68.81 REMARK 500 9 MET A 2 102.13 68.12 REMARK 500 REMARK 500 THIS ENTRY HAS 127 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 11 ARG A 15 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30432 RELATED DB: BMRB REMARK 900 CSP2-D10 DBREF 6COT A 1 17 UNP P72507 CSP2_STRPN 25 41 SEQRES 1 A 17 GLU MET ARG ILE SER ARG ILE ILE LEU DAS PHE LEU PHE SEQRES 2 A 17 LEU ARG LYS LYS MODRES 6COT DAS A 10 ASP MODIFIED RESIDUE HET DAS A 10 12 HETNAM DAS D-ASPARTIC ACID FORMUL 1 DAS C4 H7 N O4 HELIX 1 AA1 LEU A 12 LYS A 17 1 6 LINK C LEU A 9 N DAS A 10 1555 1555 1.32 LINK C DAS A 10 N PHE A 11 1555 1555 1.33 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