HEADER ANTIMICROBIAL PROTEIN 16-JUN-09 2KK9 TITLE ANTI-GROUP A STREPTOCOCCAL VACCINE EPITOPE: STRUCTURE, STABILITY AND TITLE 2 ITS ABILITY TO INTERACT WITH HLA CLASS II MOLECULES COMPND MOL_ID: 1; COMPND 2 MOLECULE: M PROTEIN, SEROTYPE 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 300-354; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: A 55-MER-LONG SYNTHETIC PEPTIDE KEYWDS S. PYOGENES, M5 PROTEIN, SYNTHETIC PEPTIDE VACCINE, CELL WALL, KEYWDS 2 PEPTIDOGLYCAN-ANCHOR, PHAGOCYTOSIS, SECRETED, VIRULENCE, UNKNOWN KEYWDS 3 FUNCTION, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR AUTHOR L.GUILHERME,M.P.ALBA,M.E.PATARROYO,J.KALIL REVDAT 3 23-MAR-11 2KK9 1 JRNL REVDAT 2 05-JAN-11 2KK9 1 JRNL REVDAT 1 16-JUN-10 2KK9 0 JRNL AUTH L.GUILHERME,M.P.ALBA,F.M.FERREIRA,S.E.OSHIRO,F.HIGA, JRNL AUTH 2 M.E.PATARROYO,J.KALIL JRNL TITL ANTI-GROUP A STREPTOCOCCAL VACCINE EPITOPE: STRUCTURE, JRNL TITL 2 STABILITY, AND ITS ABILITY TO INTERACT WITH HLA CLASS II JRNL TITL 3 MOLECULES. JRNL REF J.BIOL.CHEM. V. 286 6989 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21169359 JRNL DOI 10.1074/JBC.M110.132118 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KK9 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB101224. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 3.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 5.4 MG/ML, TRIFLUOROETHANOL/ REMARK 210 WATER 30/70% REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 ARG A 46 H LYS A 50 2.00 REMARK 500 O LYS A 50 H VAL A 52 2.15 REMARK 500 O GLU A 25 H LYS A 29 2.16 REMARK 500 O ARG A 11 H LYS A 15 2.16 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 GLU A 12 CD GLU A 12 OE2 0.120 REMARK 500 GLU A 18 CD GLU A 18 OE2 0.120 REMARK 500 GLU A 20 CD GLU A 20 OE2 0.120 REMARK 500 GLU A 25 CD GLU A 25 OE2 0.120 REMARK 500 GLU A 26 CD GLU A 26 OE2 0.120 REMARK 500 GLU A 32 CD GLU A 32 OE2 0.120 REMARK 500 GLU A 47 CD GLU A 47 OE2 0.119 REMARK 500 GLU A 53 CD GLU A 53 OE2 0.120 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 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 6 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 8 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 41 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 43 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.7 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 LEU A 3 68.13 -106.72 REMARK 500 ASP A 6 -56.15 -169.16 REMARK 500 ALA A 9 60.90 65.44 REMARK 500 ARG A 11 -62.01 -127.30 REMARK 500 ALA A 33 77.07 60.29 REMARK 500 SER A 34 68.45 -101.10 REMARK 500 ARG A 39 -129.02 -137.21 REMARK 500 ALA A 44 -72.86 -90.10 REMARK 500 SER A 45 -121.13 -127.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 2KK9 A 1 55 UNP P02977 M5_STRP5 300 354 SEQADV 2KK9 NH2 A 56 UNP P02977 AMIDATION SEQRES 1 A 56 LYS GLY LEU ARG ARG ASP LEU ASP ALA SER ARG GLU ALA SEQRES 2 A 56 LYS LYS GLN LEU GLU ALA GLU GLN GLN LYS LEU GLU GLU SEQRES 3 A 56 GLN ASN LYS ILE SER GLU ALA SER ARG LYS GLY LEU ARG SEQRES 4 A 56 ARG ASP LEU ASP ALA SER ARG GLU ALA LYS LYS GLN VAL SEQRES 5 A 56 GLU LYS ALA NH2 HET NH2 A 56 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 1 ARG A 11 SER A 34 1 24 LINK C ALA A 55 N NH2 A 56 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 MASTER 160 0 1 1 0 0 0 6 0 0 0 5 END