HEADER ANTIMICROBIAL PROTEIN 13-FEB-26 23RI TITLE L-ALANOYL-D-GLUTAMATE PEPTIDASE BACTERIOPHAGE RB49 COMLPEX WITH ZN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE M15C DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-ALANOYL-D-GLUTAMATE PEPTIDASE (ENDOLYSIN) BACTERIOPHAGE COMPND 5 RB49; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ZN2+ CONTAINING FORM. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE RB49; SOURCE 3 ORGANISM_TAXID: 50948; SOURCE 4 GENE: RB49ORF102C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS L-ALANOYL-D-GLUTAMATE PEPTIDASE, BACTERIOPHAGE RB49, ENDOLYSIN, ZN2+ KEYWDS 2 CONTAINING FORM, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.A.PROKHOROV,G.V.MIKOULINSKAIA REVDAT 1 25-FEB-26 23RI 0 JRNL AUTH D.A.PROKHOROV,G.V.MIKOULINSKAIA JRNL TITL SPATIAL STRUCTURE OF L-ALANOYL-D-GLUTAMATE PEPTIDASE OF JRNL TITL 2 BACTERIOPHAGE RB49 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 23RI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1300070255. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.05 REMARK 210 IONIC STRENGTH : 28 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 L-ALANOYL-D-GLUTAMATE PEPTIDASE, REMARK 210 25 MM [U-100% 2H] SODIUM ACETATE, REMARK 210 1 MM ZN(NO3)2, 0.03 % W/W REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 -ALI; 3D BEST TROSY HNCACB; 3D REMARK 210 BEST TROSY HN(CO)CACB; 3D BEST REMARK 210 TROSY HNCO; 3D BEST TROSY HN(CA) REMARK 210 CO; 3D BEST TROSY (H)N(COCA)NH; REMARK 210 3D H(C)CH-TOCSY ALI; 3D (H)CCH- REMARK 210 TOCSY ALI; 3D TROSY-(H)CCH-COSY REMARK 210 ARO; 2D (HB)CB(CGCC-TOCSY)HAR; REMARK 210 3D 1H-15N TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA RELEASE: 1.8.4.2, TOPSPIN REMARK 210 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 LYS A 59 42.84 -93.04 REMARK 500 1 ASP A 78 64.79 -100.78 REMARK 500 1 ASP A 108 -35.06 -133.76 REMARK 500 1 LYS A 113 57.07 28.97 REMARK 500 1 PRO A 116 68.27 -69.78 REMARK 500 2 ASP A 78 65.76 -100.85 REMARK 500 2 LYS A 113 49.06 36.06 REMARK 500 2 PRO A 116 70.19 -69.81 REMARK 500 3 LYS A 59 56.71 -149.01 REMARK 500 3 ASP A 78 66.63 -100.85 REMARK 500 3 ASP A 108 -33.02 -130.92 REMARK 500 3 LYS A 113 56.69 33.64 REMARK 500 3 PRO A 116 71.95 -69.76 REMARK 500 4 ASP A 78 64.98 -100.04 REMARK 500 4 ASP A 108 -30.71 -130.01 REMARK 500 4 LYS A 113 56.11 34.85 REMARK 500 4 PRO A 116 71.57 -69.72 REMARK 500 4 TYR A 125 77.95 -115.58 REMARK 500 5 ASP A 108 -32.56 -131.63 REMARK 500 5 LYS A 113 50.52 33.31 REMARK 500 5 PRO A 116 70.22 -69.84 REMARK 500 6 LYS A 59 54.21 -143.74 REMARK 500 6 ASP A 78 68.07 -100.97 REMARK 500 6 LYS A 113 48.41 36.36 REMARK 500 6 PRO A 116 69.80 -69.75 REMARK 500 7 LYS A 59 54.44 -105.67 REMARK 500 7 ASP A 78 65.35 -100.87 REMARK 500 7 LYS A 113 48.85 34.48 REMARK 500 7 PRO A 116 71.35 -69.79 REMARK 500 8 ASP A 78 67.89 -101.06 REMARK 500 8 ASP A 108 -35.65 -135.68 REMARK 500 8 LYS A 113 56.92 26.56 REMARK 500 8 PRO A 116 70.32 -69.67 REMARK 500 9 LYS A 59 39.22 -94.69 REMARK 500 9 ASP A 78 65.47 -100.10 REMARK 500 9 LYS A 113 58.81 37.54 REMARK 500 9 ASP A 114 74.51 -106.11 REMARK 500 9 PRO A 116 70.11 -69.75 REMARK 500 10 ASP A 78 70.78 -101.29 REMARK 500 10 ASP A 108 -32.91 -132.47 REMARK 500 10 LYS A 113 52.86 33.48 REMARK 500 10 PRO A 116 71.66 -69.74 REMARK 500 10 TYR A 125 77.91 -116.64 REMARK 500 11 ASP A 78 65.29 -100.70 REMARK 500 11 ASP A 108 -30.90 -130.23 REMARK 500 11 LYS A 113 49.20 34.04 REMARK 500 11 PRO A 116 71.33 -69.71 REMARK 500 12 LYS A 59 57.99 -100.95 REMARK 500 12 ASP A 78 65.75 -100.99 REMARK 500 12 LYS A 113 60.36 36.84 REMARK 500 REMARK 500 THIS ENTRY HAS 88 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VO9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE REMARK 900 LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500 REMARK 900 RELATED ID: 2MXZ RELATED DB: PDB REMARK 900 BACTERIOPHAGE T5 L-ALANOYL-D-GLUTAMATE PEPTIDASE COMLPEX WITH ZN2+ REMARK 900 RELATED ID: 8P3A RELATED DB: PDB REMARK 900 BACTERIOPHAGE T5 L-ALANOYL-D-GLUTAMATE PEPTIDASE ZN2+/CA2+ FORM REMARK 900 RELATED ID: 8Q2G RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF LYSECD7 ENDOLYSIN AGAINST GRAM-NEGATIVE BACTERIA REMARK 900 RELATED ID: 5OPZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERRATIA MARCESCENS L-ALA D-GLU ENDOPEPTIDASE REMARK 900 CHIX REMARK 900 RELATED ID: 6AKV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LYSB4, THE ENDOLYSIN FROM BACILLUS CEREUS- REMARK 900 TARGETING BACTERIOPHAGE B4 REMARK 900 RELATED ID: 36831 RELATED DB: BMRB REMARK 900 L-ALANOYL-D-GLUTAMATE PEPTIDASE BACTERIOPHAGE RB49 COMLPEX WITH ZN2+ DBREF 23RI A 1 129 UNP Q7Y3Q4 Q7Y3Q4_BPRB4 1 129 SEQRES 1 A 129 MET PHE LYS LEU SER GLN ARG SER LYS ASP ARG LEU VAL SEQRES 2 A 129 GLY VAL HIS PRO ASP LEU VAL LYS VAL VAL HIS ARG ALA SEQRES 3 A 129 LEU GLU LEU THR PRO VAL ASP PHE GLY ILE THR GLU GLY SEQRES 4 A 129 VAL ARG SER LEU GLU THR GLN LYS LYS TYR VAL ALA GLU SEQRES 5 A 129 GLY LYS SER LYS THR MET LYS SER ARG HIS LEU HIS GLY SEQRES 6 A 129 PHE ALA VAL ASP VAL VAL ALA TYR PRO LYS ASP LYS ASP SEQRES 7 A 129 THR TRP ASN MET LYS TYR TYR ARG MET ILE ALA ASP ALA SEQRES 8 A 129 PHE LYS GLN ALA GLY ARG GLU LEU GLY VAL PRO VAL GLU SEQRES 9 A 129 TRP GLY GLY ASP TRP THR SER PHE LYS ASP GLY PRO HIS SEQRES 10 A 129 LEU GLN LEU PRO HIS SER LYS TYR PRO ASP PRO LYS HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 AA1 SER A 5 LEU A 12 1 8 HELIX 2 AA2 HIS A 16 LEU A 29 1 14 HELIX 3 AA3 SER A 42 GLU A 52 1 11 HELIX 4 AA4 SER A 60 GLY A 65 5 6 HELIX 5 AA5 ASN A 81 GLY A 100 1 20 HELIX 6 AA6 PRO A 121 TYR A 125 5 5 SHEET 1 AA1 4 PHE A 34 GLY A 39 0 SHEET 2 AA1 4 ALA A 67 ALA A 72 -1 O ASP A 69 N GLU A 38 SHEET 3 AA1 4 LEU A 118 GLN A 119 -1 O LEU A 118 N VAL A 68 SHEET 4 AA1 4 GLU A 104 TRP A 105 -1 N GLU A 104 O GLN A 119 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 170 0 1 6 4 0 0 6 1042 1 0 10 END