HEADER BIOSYNTHETIC PROTEIN 21-MAR-19 6OC2 TITLE CSP1-CYC(ORN6D10) 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 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 4 ORGANISM_TAXID: 1313 KEYWDS MODULATOR FOR PNEUMOCOCCAL QUORUM SENSING, SYNTHETIC CYCLIC PEPTIDE, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.YANG REVDAT 4 14-JUN-23 6OC2 1 LINK REVDAT 3 05-FEB-20 6OC2 1 JRNL REVDAT 2 22-JAN-20 6OC2 1 JRNL REVDAT 1 08-JAN-20 6OC2 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 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TORSION ANGLE DYNAMICS WITH EEFX REMARK 3 REFINEMENT REMARK 4 REMARK 4 6OC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000240388. 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-CYC(ORN6D10), 250 MM REMARK 210 DEUTERIUM DPC, 137 MM SODIUM REMARK 210 CHLORIDE, 2.7 MM POTASSIUM REMARK 210 CHLORIDE, 10 MM NA2HPO4, 1.8 MM REMARK 210 KH2PO4, 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 18 PHE A 7 CB - CG - CD2 ANGL. DEV. = 4.6 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 MET A 2 -178.92 68.55 REMARK 500 1 SER A 5 -115.23 45.26 REMARK 500 1 PHE A 7 -114.92 -66.26 REMARK 500 1 ILE A 12 -128.86 -161.85 REMARK 500 1 LEU A 13 -27.37 161.36 REMARK 500 2 SER A 5 -100.86 58.80 REMARK 500 2 PHE A 7 -112.59 13.71 REMARK 500 2 PHE A 11 -68.99 -96.09 REMARK 500 2 ILE A 12 -34.45 -173.61 REMARK 500 2 LEU A 13 -27.85 84.89 REMARK 500 3 ORN A 6 -20.29 77.67 REMARK 500 3 PHE A 7 -102.60 4.50 REMARK 500 3 PHE A 11 -62.26 -109.72 REMARK 500 3 ILE A 12 -121.40 -161.34 REMARK 500 3 LEU A 13 -18.22 166.22 REMARK 500 3 GLN A 14 -162.84 81.41 REMARK 500 3 ARG A 15 -74.36 74.23 REMARK 500 4 SER A 5 -104.65 60.73 REMARK 500 4 PHE A 7 -113.83 17.97 REMARK 500 4 PHE A 11 -77.51 -105.74 REMARK 500 4 LEU A 13 56.99 175.64 REMARK 500 5 LEU A 4 -34.64 84.49 REMARK 500 5 SER A 5 -116.17 61.89 REMARK 500 5 PHE A 7 -105.20 -10.00 REMARK 500 5 PHE A 11 -68.64 -94.39 REMARK 500 5 ILE A 12 -28.97 -174.87 REMARK 500 5 LEU A 13 -36.07 82.15 REMARK 500 5 GLN A 14 -12.74 71.85 REMARK 500 6 SER A 5 -112.86 62.00 REMARK 500 6 PHE A 7 -108.28 5.93 REMARK 500 6 PHE A 11 -75.92 -107.62 REMARK 500 6 LEU A 13 62.69 -174.90 REMARK 500 6 GLN A 14 -108.58 -92.22 REMARK 500 7 SER A 5 -107.90 61.72 REMARK 500 7 PHE A 7 -108.77 9.46 REMARK 500 7 PHE A 11 -78.23 -103.58 REMARK 500 7 LEU A 13 58.09 178.79 REMARK 500 8 PHE A 7 -108.70 -77.17 REMARK 500 8 ILE A 12 -124.95 -163.51 REMARK 500 8 LEU A 13 -22.42 166.35 REMARK 500 8 GLN A 14 160.99 81.67 REMARK 500 8 ARG A 15 -62.63 81.22 REMARK 500 9 ARG A 3 -49.81 -130.36 REMARK 500 9 SER A 5 77.67 40.22 REMARK 500 9 ORN A 6 -22.52 76.69 REMARK 500 9 PHE A 7 -110.63 21.02 REMARK 500 9 PHE A 11 -78.51 -117.17 REMARK 500 9 LEU A 13 39.38 173.92 REMARK 500 10 SER A 5 -114.86 61.04 REMARK 500 10 PHE A 7 -104.86 -4.11 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30594 RELATED DB: BMRB REMARK 900 CSP1-CYC(ORN6D10) REMARK 999 REMARK 999 SEQUENCE REMARK 999 ORN AND ASP ARE CHEMICALLY ADDED TO THE SEQUENCE ON 6TH AND 10TH REMARK 999 POSITIONS, AND THEN CYCLIZED. HOWEVER, DURING STRUCTURE CALCULATION, REMARK 999 THE 10TH RESIDUE IS LABELED AS ASN FOR CONVENIENCE TO CONSTRUCT REMARK 999 THE MACROCYCLE AND ASN10 IS KEPT IN THE FINAL COORDINATE AND REMARK 999 CHEMICAL SHIFT FILE FOR CONSISTENCY. THE ACTUAL SEQUENCE IS STILL: REMARK 999 EMRLS(ORN)FFR(ASP)FILQRKK. DBREF 6OC2 A 1 17 UNP P60242 CSP1_STREE 25 41 SEQADV 6OC2 ORN A 6 UNP P60242 LYS 30 ENGINEERED MUTATION SEQADV 6OC2 ASN A 10 UNP P60242 ASP 34 ENGINEERED MUTATION SEQRES 1 A 17 GLU MET ARG LEU SER ORN PHE PHE ARG ASN PHE ILE LEU SEQRES 2 A 17 GLN ARG LYS LYS HET ORN A 6 15 HETNAM ORN L-ORNITHINE FORMUL 1 ORN C5 H12 N2 O2 LINK C SER A 5 N ORN A 6 1555 1555 1.36 LINK C ORN A 6 N PHE A 7 1555 1555 1.35 LINK CD ORN A 6 ND2 ASN A 10 1555 1555 1.50 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