HEADER ANTIMICROBIAL PROTEIN 17-MAY-23 8P3A TITLE BACTERIOPHAGE T5 L-ALANOYL-D-GLUTAMATE PEPTIDASE ZN2+/CA2+ FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-ALANYL-D-GLUTAMATE PEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDOLYSIN,LYSOZYME; COMPND 5 EC: 3.4.24.-; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ZN - ZN2+ ION CA - CA2+ ION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T5; SOURCE 3 ORGANISM_TAXID: 2695836; SOURCE 4 GENE: LYS, T5.040, T5P039, ORF10C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET3A KEYWDS L-ALANOYL-D-GLUTAMATE PEPTIDASE, BACTERIOPHAGE T5, ENDOLYSIN, ZN2+ KEYWDS 2 AND CA2+ CONTAINING FORM, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.A.PROKHOROV,V.P.KUTYSHENKO,G.V.MIKOULINSKAIA REVDAT 1 05-JUL-23 8P3A 0 JRNL AUTH D.A.PROKHOROV,G.V.MIKOULINSKAIA,N.V.MOLOCHKOV,V.N.UVERSKY, JRNL AUTH 2 V.P.KUTYSHENKO JRNL TITL MECHANISM OF CA2+-DEPENDENT ACTIVATION OF JRNL TITL 2 L-ALANOYL-D-GLUTAMATE PEPTIDASE BACTERIOPHAGE T5. 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 8P3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292129923. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.1 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 L-ALANOYL-D-GLUTAMATE PEPTIDASE, REMARK 210 50 MM [U-100% 2H] SODIUM ACETATE, REMARK 210 3 MM ZN(NO3)2, 3 MM CACL2, 0.03 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 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 C(CO)NH; 3D 1H-15N TOCSY; 3D REMARK 210 HCCH-TOCSY; 2D CBHD; 3D HNCO; 2D REMARK 210 1H-13C HSQC AROMATIC; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-15N NOESY; REMARK 210 3D HN(CO)CA; 3D 1H-13C NOESY REMARK 210 AROMATIC 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 : TARGET FUNCTION 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: 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 PHE A 3 -168.22 -69.86 REMARK 500 1 ILE A 51 -64.79 -98.38 REMARK 500 1 ALA A 52 61.73 70.20 REMARK 500 1 ASN A 53 28.59 -171.00 REMARK 500 1 THR A 55 80.29 35.83 REMARK 500 1 ASP A 60 60.69 -174.40 REMARK 500 1 PRO A 61 -170.02 -69.73 REMARK 500 1 LYS A 63 30.84 -93.86 REMARK 500 1 ALA A 71 134.38 158.97 REMARK 500 1 ALA A 112 34.36 178.01 REMARK 500 1 ASP A 119 154.85 179.48 REMARK 500 1 TYR A 120 27.59 -152.45 REMARK 500 1 ASP A 130 46.84 35.18 REMARK 500 2 PHE A 3 -169.00 -64.29 REMARK 500 2 PRO A 18 -178.56 -69.80 REMARK 500 2 LEU A 30 27.31 -140.48 REMARK 500 2 ILE A 51 -65.87 -97.60 REMARK 500 2 ALA A 52 53.21 71.23 REMARK 500 2 ASN A 53 15.69 -144.44 REMARK 500 2 THR A 55 49.43 36.52 REMARK 500 2 ASP A 60 58.81 179.89 REMARK 500 2 PRO A 61 -169.60 -69.78 REMARK 500 2 ALA A 71 133.75 158.49 REMARK 500 2 ASP A 86 87.74 -66.52 REMARK 500 2 ALA A 112 31.52 174.21 REMARK 500 2 TYR A 120 -38.37 -154.72 REMARK 500 2 ASP A 130 104.19 -42.39 REMARK 500 3 PHE A 3 -169.46 -64.90 REMARK 500 3 LEU A 30 26.25 -140.08 REMARK 500 3 ILE A 51 -64.10 -96.96 REMARK 500 3 ASN A 53 23.07 -157.11 REMARK 500 3 THR A 55 49.77 36.58 REMARK 500 3 LYS A 59 -56.93 -125.02 REMARK 500 3 ASP A 60 62.56 -165.19 REMARK 500 3 PRO A 61 -170.36 -69.80 REMARK 500 3 SER A 62 -169.30 -102.19 REMARK 500 3 LYS A 63 41.01 -94.22 REMARK 500 3 ALA A 71 132.45 160.95 REMARK 500 3 ALA A 112 31.83 175.48 REMARK 500 3 TYR A 120 -39.87 -155.94 REMARK 500 3 ASP A 130 104.99 -44.40 REMARK 500 4 PHE A 3 -168.72 -64.00 REMARK 500 4 PRO A 18 -179.14 -69.69 REMARK 500 4 LEU A 30 26.29 -140.54 REMARK 500 4 ILE A 51 -68.68 -96.94 REMARK 500 4 ALA A 52 54.70 71.43 REMARK 500 4 ASN A 53 16.03 -145.03 REMARK 500 4 THR A 55 49.07 36.47 REMARK 500 4 LYS A 59 -40.45 -133.56 REMARK 500 4 ASP A 60 62.85 -174.37 REMARK 500 REMARK 500 THIS ENTRY HAS 300 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 113 OD1 REMARK 620 2 ASN A 115 OD1 57.7 REMARK 620 3 SER A 117 OG 69.0 74.0 REMARK 620 N 1 2 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: 34817 RELATED DB: BMRB REMARK 900 BACTERIOPHAGE T5 L-ALANOYL-D-GLUTAMATE PEPTIDASE ZN2+/CA2+ FORM DBREF 8P3A A 1 137 UNP Q6QGP7 ENLYS_BPT5 1 137 SEQRES 1 A 137 MET SER PHE LYS PHE GLY LYS ASN SER GLU LYS GLN LEU SEQRES 2 A 137 ALA THR VAL LYS PRO GLU LEU GLN LYS VAL ALA ARG ARG SEQRES 3 A 137 ALA LEU GLU LEU SER PRO TYR ASP PHE THR ILE VAL GLN SEQRES 4 A 137 GLY ILE ARG THR VAL ALA GLN SER ALA GLN ASN ILE ALA SEQRES 5 A 137 ASN GLY THR SER PHE LEU LYS ASP PRO SER LYS SER LYS SEQRES 6 A 137 HIS ILE THR GLY ASP ALA ILE ASP PHE ALA PRO TYR ILE SEQRES 7 A 137 ASN GLY LYS ILE ASP TRP ASN ASP LEU GLU ALA PHE TRP SEQRES 8 A 137 ALA VAL LYS LYS ALA PHE GLU GLN ALA GLY LYS GLU LEU SEQRES 9 A 137 GLY ILE LYS LEU ARG PHE GLY ALA ASP TRP ASN ALA SER SEQRES 10 A 137 GLY ASP TYR HIS ASP GLU ILE LYS ARG GLY THR TYR ASP SEQRES 11 A 137 GLY GLY HIS VAL GLU LEU VAL HET ZN A 201 1 HET CA A 202 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 CA CA 2+ HELIX 1 AA1 GLY A 6 THR A 15 1 10 HELIX 2 AA2 GLU A 19 LEU A 30 1 12 HELIX 3 AA3 THR A 43 ILE A 51 1 9 HELIX 4 AA4 LYS A 65 GLY A 69 5 5 HELIX 5 AA5 ASP A 86 GLY A 105 1 20 HELIX 6 AA6 ASP A 122 GLY A 127 5 6 SHEET 1 AA1 3 ASP A 34 GLN A 39 0 SHEET 2 AA1 3 ILE A 72 ILE A 78 -1 O ASP A 73 N GLN A 39 SHEET 3 AA1 3 LYS A 81 ILE A 82 -1 O LYS A 81 N ILE A 78 SHEET 1 AA2 4 ASP A 34 GLN A 39 0 SHEET 2 AA2 4 ILE A 72 ILE A 78 -1 O ASP A 73 N GLN A 39 SHEET 3 AA2 4 HIS A 133 LEU A 136 -1 O VAL A 134 N ILE A 72 SHEET 4 AA2 4 LEU A 108 GLY A 111 -1 N GLY A 111 O HIS A 133 LINK OD1 ASP A 113 CA CA A 202 1555 1555 3.13 LINK OD1 ASN A 115 CA CA A 202 1555 1555 3.05 LINK OG SER A 117 CA CA A 202 1555 1555 3.06 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