HEADER BIOSYNTHETIC PROTEIN 20-NOV-19 6V1N TITLE CSP1-E1A-CYC(DAP6E10) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPETENCE-STIMULATING PEPTIDE TYPE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CSP-1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: DPP AND GLU WERE CHEMICALLY ADDED TO THE 6TH AND 10TH COMPND 8 POSITIONS AND THEN CYCLIZED. HOWEVER, DURING STRUCTURE CALCULATION, COMPND 9 GLU10 WAS LABELED AS GLN10 TO CONSTRUCT THE MACROCYCLE FOR COMPND 10 CONVENIENCE. GLN10 WAS KEPT IN THE FINAL COORDINATE FILE AND CHEMICAL COMPND 11 SHIFT FILE FOR CONSISTENCY. THE ACTUAL SEQUENCE IS STILL: AMRLS(DPP) COMPND 12 FFR(GLU)FILQRKK SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 4 ORGANISM_TAXID: 1313 KEYWDS MODULATOR, QUORUM SENSING, BIOSYNTHETIC PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.YANG REVDAT 3 05-FEB-20 6V1N 1 JRNL REVDAT 2 22-JAN-20 6V1N 1 JRNL REVDAT 1 08-JAN-20 6V1N 0 JRNL AUTH Y.YANG,J.LIN,A.HARRINGTON,G.CORNILESCU,G.W.LAU,Y.TAL-GAN JRNL TITL DESIGNING CYCLIC COMPETENCE-STIMULATING PEPTIDE (CSP) JRNL TITL 2 ANALOGS WITH PAN-GROUP QUORUM-SENSING INHIBITION ACTIVITY JRNL TITL 3 INSTREPTOCOCCUS PNEUMONIAE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 1689 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 31915298 JRNL DOI 10.1073/PNAS.1915812117 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS (X-PLOR NIH), KUSZEWSKI (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WITH EEFX REFINEMENT REMARK 4 REMARK 4 6V1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245599. 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 : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.9 MM CSP1-E1A-CYC(DAP6E10), REMARK 210 250 MM DEUTERIUM DPC, 137 MM REMARK 210 SODIUM CHLORIDE, 2.7 MM REMARK 210 POTASSIUM CHLORIDE, 10 MM REMARK 210 NA2HPO4, 1.8 MM KH2PO4, 90% H2O/ REMARK 210 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-13C HSQC; REMARK 210 2D 1H-15N 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 : 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 O LEU A 13 H LYS A 17 1.53 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 3 PHE A 11 CB PHE A 11 CG -0.104 REMARK 500 13 PHE A 11 CB PHE A 11 CG -0.103 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 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 LEU A 13 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 2 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 3 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 3 LEU A 13 N - CA - CB ANGL. DEV. = -14.0 DEGREES REMARK 500 4 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 4 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 5 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 5 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 6 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 6 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 7 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 7 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 8 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 8 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 9 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 9 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 10 PHE A 8 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 10 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 11 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 11 LEU A 13 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 12 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 12 LEU A 13 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 13 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 13 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 14 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 14 LEU A 13 N - CA - CB ANGL. DEV. = -13.1 DEGREES REMARK 500 15 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 15 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 16 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 16 LEU A 13 N - CA - CB ANGL. DEV. = -14.0 DEGREES REMARK 500 17 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 17 LEU A 13 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 18 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 18 LEU A 13 N - CA - CB ANGL. DEV. = -14.0 DEGREES REMARK 500 19 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 19 LEU A 13 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 20 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 20 LEU A 13 N - CA - CB ANGL. DEV. = -14.0 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 LEU A 4 99.08 -43.94 REMARK 500 1 SER A 5 -81.03 -99.70 REMARK 500 1 DPP A 6 30.94 -74.33 REMARK 500 1 PHE A 8 135.16 84.62 REMARK 500 1 GLN A 10 4.47 -172.22 REMARK 500 1 PHE A 11 -37.09 -146.55 REMARK 500 2 LEU A 4 98.32 -38.25 REMARK 500 2 SER A 5 -81.50 -94.24 REMARK 500 2 DPP A 6 29.89 -74.28 REMARK 500 2 PHE A 8 135.15 84.84 REMARK 500 2 GLN A 10 4.29 -172.41 REMARK 500 2 PHE A 11 -37.45 -146.19 REMARK 500 3 ARG A 3 -36.80 172.74 REMARK 500 3 LEU A 4 93.95 -47.21 REMARK 500 3 PHE A 8 134.85 86.20 REMARK 500 3 GLN A 10 4.73 -170.33 REMARK 500 3 PHE A 11 -38.73 -147.20 REMARK 500 4 ARG A 3 -37.12 173.00 REMARK 500 4 LEU A 4 98.05 -49.51 REMARK 500 4 SER A 5 -80.42 -93.87 REMARK 500 4 DPP A 6 29.85 -75.43 REMARK 500 4 PHE A 8 135.10 84.50 REMARK 500 4 GLN A 10 3.96 -172.09 REMARK 500 4 PHE A 11 -37.97 -145.47 REMARK 500 5 LEU A 4 95.91 -32.48 REMARK 500 5 PHE A 8 134.36 85.95 REMARK 500 5 GLN A 10 4.59 -171.29 REMARK 500 5 PHE A 11 -39.66 -145.41 REMARK 500 6 ARG A 3 -37.27 173.34 REMARK 500 6 LEU A 4 98.31 -48.33 REMARK 500 6 SER A 5 -84.44 -91.45 REMARK 500 6 DPP A 6 30.47 -73.73 REMARK 500 6 PHE A 8 135.09 84.77 REMARK 500 6 GLN A 10 4.39 -172.34 REMARK 500 6 PHE A 11 -37.65 -146.08 REMARK 500 7 ARG A 3 -36.56 172.38 REMARK 500 7 LEU A 4 98.18 -49.94 REMARK 500 7 SER A 5 -82.28 -92.86 REMARK 500 7 DPP A 6 30.30 -74.35 REMARK 500 7 PHE A 8 135.08 84.49 REMARK 500 7 GLN A 10 3.98 -172.38 REMARK 500 7 PHE A 11 -37.77 -145.34 REMARK 500 8 LEU A 4 97.98 -35.69 REMARK 500 8 SER A 5 -80.33 -94.38 REMARK 500 8 DPP A 6 29.74 -75.41 REMARK 500 8 PHE A 8 135.06 84.64 REMARK 500 8 GLN A 10 4.64 -172.14 REMARK 500 8 PHE A 11 -38.10 -146.05 REMARK 500 9 LEU A 4 99.23 -35.75 REMARK 500 9 SER A 5 -83.85 -93.63 REMARK 500 REMARK 500 THIS ENTRY HAS 125 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 PHE A 8 0.09 SIDE CHAIN REMARK 500 2 PHE A 8 0.09 SIDE CHAIN REMARK 500 3 PHE A 8 0.09 SIDE CHAIN REMARK 500 4 PHE A 8 0.09 SIDE CHAIN REMARK 500 5 PHE A 8 0.09 SIDE CHAIN REMARK 500 6 PHE A 8 0.09 SIDE CHAIN REMARK 500 7 PHE A 8 0.09 SIDE CHAIN REMARK 500 8 PHE A 8 0.09 SIDE CHAIN REMARK 500 9 PHE A 8 0.09 SIDE CHAIN REMARK 500 10 PHE A 8 0.09 SIDE CHAIN REMARK 500 11 PHE A 8 0.09 SIDE CHAIN REMARK 500 12 PHE A 8 0.09 SIDE CHAIN REMARK 500 13 PHE A 8 0.09 SIDE CHAIN REMARK 500 14 PHE A 8 0.09 SIDE CHAIN REMARK 500 15 PHE A 8 0.09 SIDE CHAIN REMARK 500 16 PHE A 8 0.09 SIDE CHAIN REMARK 500 17 PHE A 8 0.09 SIDE CHAIN REMARK 500 18 PHE A 8 0.09 SIDE CHAIN REMARK 500 19 PHE A 8 0.09 SIDE CHAIN REMARK 500 20 PHE A 8 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30690 RELATED DB: BMRB REMARK 900 CSP1-E1A-CYC(DAP6E10) REMARK 999 REMARK 999 SEQUENCE REMARK 999 DPP AND GLU WERE CHEMICALLY ADDED TO THE 6TH AND 10TH POSITIONS AND REMARK 999 THEN CYCLIZED. HOWEVER, DURING STRUCTURE CALCULATION, GLU10 WAS REMARK 999 LABELED AS GLN10 TO CONSTRUCT THE MACROCYCLE FOR CONVENIENCE. GLN10 REMARK 999 WAS KEPT IN THE FINAL COORDINATE FILE AND CHEMICAL SHIFT FILE FOR REMARK 999 CONSISTENCY. THE ACTUAL SEQUENCE IS STILL: AMRLS(DPP)FFR(GLU)FILQRKK DBREF 6V1N A 1 17 UNP P60242 CSP1_STREE 25 41 SEQADV 6V1N ALA A 1 UNP P60242 GLU 25 ENGINEERED MUTATION SEQADV 6V1N DPP A 6 UNP P60242 LYS 30 ENGINEERED MUTATION SEQADV 6V1N GLN A 10 UNP P60242 ASP 34 ENGINEERED MUTATION SEQRES 1 A 17 ALA MET ARG LEU SER DPP PHE PHE ARG GLN PHE ILE LEU SEQRES 2 A 17 GLN ARG LYS LYS HET DPP A 6 9 HETNAM DPP DIAMINOPROPANOIC ACID FORMUL 1 DPP C3 H8 N2 O2 LINK C SER A 5 N DPP A 6 1555 1555 1.37 LINK C DPP A 6 N PHE A 7 1555 1555 1.35 LINK CB DPP A 6 NE2 GLN A 10 1555 1555 1.54 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