HEADER HYDROLASE 24-JAN-14 2MK5 TITLE SOLUTION STRUCTURE OF A PROTEIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOLYSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 368-495; COMPND 5 SYNONYM: PUTATIVE LYSIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PHAGE GH15; SOURCE 3 ORGANISM_TAXID: 760530; SOURCE 4 GENE: LYSGH15, GH15_071; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PMCSG7 KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.FENG,J.GU REVDAT 2 18-DEC-19 2MK5 1 JRNL REMARK SEQADV REVDAT 1 28-MAY-14 2MK5 0 JRNL AUTH J.GU,Y.FENG,X.FENG,C.SUN,L.LEI,W.DING,F.NIU,L.JIAO,M.YANG, JRNL AUTH 2 Y.LI,X.LIU,J.SONG,Z.CUI,D.HAN,C.DU,Y.YANG,S.OUYANG,Z.J.LIU, JRNL AUTH 3 W.HAN JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION REVEALS LYSGH15 JRNL TITL 2 AS AN UNPRECEDENTED "EF-HAND-LIKE" CALCIUM-BINDING PHAGE JRNL TITL 3 LYSIN. JRNL REF PLOS PATHOG. V. 10 04109 2014 JRNL REFN ESSN 1553-7374 JRNL PMID 24831957 JRNL DOI 10.1371/JOURNAL.PPAT.1004109 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, CNS REMARK 3 AUTHORS : VARIAN (VNMRJ), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000103710. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM [U-13C; U-15N] ENTITY-1, REMARK 210 40 MM SODIUM PHOSPHATE-2, 50 MM REMARK 210 SODIUM CHLORIDE-3, 0.02 % DSS-4, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(CA)CO; 3D HBHA(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D CCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DD2 REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, CYANA, CNS REMARK 210 METHOD USED : MOLECULAR DYNAMICS, SIMULATED REMARK 210 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: 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 ALA A 3 -60.67 -100.16 REMARK 500 1 MET A 7 89.16 179.04 REMARK 500 1 SER A 12 -69.12 -159.34 REMARK 500 1 THR A 15 16.11 59.81 REMARK 500 1 VAL A 17 94.19 59.67 REMARK 500 1 LYS A 21 -88.78 62.14 REMARK 500 1 THR A 22 73.79 -158.18 REMARK 500 1 SER A 24 25.20 -146.59 REMARK 500 1 THR A 27 153.08 65.48 REMARK 500 1 ASN A 57 -45.60 79.58 REMARK 500 1 ALA A 92 109.76 -48.60 REMARK 500 1 VAL A 111 -60.53 38.86 REMARK 500 2 ALA A 3 89.47 -158.64 REMARK 500 2 MET A 7 -43.23 71.42 REMARK 500 2 THR A 22 79.84 54.97 REMARK 500 2 PRO A 28 91.72 -69.46 REMARK 500 2 ALA A 29 -39.51 -136.89 REMARK 500 2 THR A 34 132.99 73.50 REMARK 500 2 VAL A 111 -53.41 46.99 REMARK 500 3 LYS A 4 80.28 64.74 REMARK 500 3 MET A 7 -9.14 79.42 REMARK 500 3 ASP A 8 119.01 73.45 REMARK 500 3 LYS A 9 -43.58 80.18 REMARK 500 3 THR A 11 88.51 54.24 REMARK 500 3 THR A 22 84.13 82.84 REMARK 500 3 ALA A 29 -87.52 62.56 REMARK 500 3 ARG A 31 85.03 53.94 REMARK 500 3 VAL A 33 -61.63 -137.94 REMARK 500 3 THR A 34 41.84 -81.56 REMARK 500 3 SER A 36 -68.23 -167.82 REMARK 500 3 VAL A 111 -54.82 43.29 REMARK 500 4 ASN A 2 113.74 69.75 REMARK 500 4 LYS A 4 -20.28 78.18 REMARK 500 4 LYS A 9 99.89 -163.23 REMARK 500 4 THR A 11 101.82 -55.45 REMARK 500 4 LYS A 21 77.43 71.54 REMARK 500 4 ALA A 25 86.15 67.59 REMARK 500 4 THR A 27 89.86 68.16 REMARK 500 4 ALA A 29 -163.47 60.26 REMARK 500 4 ARG A 31 -52.23 -142.19 REMARK 500 4 VAL A 111 -42.30 51.19 REMARK 500 5 ASN A 5 -54.04 72.14 REMARK 500 5 TYR A 6 -65.10 70.37 REMARK 500 5 LYS A 9 -4.57 -148.14 REMARK 500 5 THR A 30 -78.34 -91.02 REMARK 500 5 PRO A 32 46.92 -89.50 REMARK 500 5 VAL A 33 98.12 -45.02 REMARK 500 5 THR A 34 -35.96 156.13 REMARK 500 5 SER A 36 28.43 -157.61 REMARK 500 5 ALA A 92 104.81 -50.37 REMARK 500 REMARK 500 THIS ENTRY HAS 190 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 2 ARG A 106 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19752 RELATED DB: BMRB REMARK 900 RELATED ID: 4OLK RELATED DB: PDB REMARK 900 RELATED ID: 4OLS RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 UNIPROT IS INCORRECT AT THIS POSITION. THE DEPOSITORS CONFIRM THAT REMARK 999 RESIDUE 469 IS ASN. DBREF 2MK5 A 4 131 UNP D6QY02 D6QY02_9CAUD 368 495 SEQADV 2MK5 SER A 1 UNP D6QY02 EXPRESSION TAG SEQADV 2MK5 ASN A 2 UNP D6QY02 EXPRESSION TAG SEQADV 2MK5 ALA A 3 UNP D6QY02 EXPRESSION TAG SEQADV 2MK5 ASN A 105 UNP D6QY02 ASP 469 SEE REMARK 999 SEQRES 1 A 131 SER ASN ALA LYS ASN TYR MET ASP LYS GLY THR SER SER SEQRES 2 A 131 SER THR VAL VAL LYS ASP GLY LYS THR SER SER ALA SER SEQRES 3 A 131 THR PRO ALA THR ARG PRO VAL THR GLY SER TRP LYS LYS SEQRES 4 A 131 ASN GLN TYR GLY THR TRP TYR LYS PRO GLU ASN ALA THR SEQRES 5 A 131 PHE VAL ASN GLY ASN GLN PRO ILE VAL THR ARG ILE GLY SEQRES 6 A 131 SER PRO PHE LEU ASN ALA PRO VAL GLY GLY ASN LEU PRO SEQRES 7 A 131 ALA GLY ALA THR ILE VAL TYR ASP GLU VAL CYS ILE GLN SEQRES 8 A 131 ALA GLY HIS ILE TRP ILE GLY TYR ASN ALA TYR ASN GLY SEQRES 9 A 131 ASN ARG VAL TYR CYS PRO VAL ARG THR CYS GLN GLY VAL SEQRES 10 A 131 PRO PRO ASN HIS ILE PRO GLY VAL ALA TRP GLY VAL PHE SEQRES 11 A 131 LYS SHEET 1 A 6 LYS A 38 LYS A 39 0 SHEET 2 A 6 TRP A 45 VAL A 54 -1 O TYR A 46 N LYS A 38 SHEET 3 A 6 THR A 82 GLN A 91 -1 O ILE A 83 N PHE A 53 SHEET 4 A 6 GLY A 93 ASN A 100 -1 O TRP A 96 N CYS A 89 SHEET 5 A 6 ARG A 112 GLY A 116 -1 O ARG A 112 N ILE A 95 SHEET 6 A 6 HIS A 121 ALA A 126 -1 O ILE A 122 N GLN A 115 SHEET 1 B 7 GLY A 75 LEU A 77 0 SHEET 2 B 7 ILE A 60 ILE A 64 -1 N ILE A 60 O LEU A 77 SHEET 3 B 7 ARG A 106 CYS A 109 -1 O TYR A 108 N ARG A 63 SHEET 4 B 7 GLY A 93 ASN A 100 -1 N TYR A 99 O VAL A 107 SHEET 5 B 7 THR A 82 GLN A 91 -1 N CYS A 89 O TRP A 96 SHEET 6 B 7 TRP A 45 VAL A 54 -1 N PHE A 53 O ILE A 83 SHEET 7 B 7 VAL A 129 LYS A 131 -1 O VAL A 129 N VAL A 54 CISPEP 1 PRO A 118 PRO A 119 1 -0.62 CISPEP 2 PRO A 118 PRO A 119 2 1.24 CISPEP 3 PRO A 118 PRO A 119 3 0.91 CISPEP 4 PRO A 118 PRO A 119 4 1.54 CISPEP 5 PRO A 118 PRO A 119 5 0.20 CISPEP 6 PRO A 118 PRO A 119 6 8.44 CISPEP 7 PRO A 118 PRO A 119 7 1.19 CISPEP 8 PRO A 118 PRO A 119 8 -0.45 CISPEP 9 PRO A 118 PRO A 119 9 1.85 CISPEP 10 PRO A 118 PRO A 119 10 0.07 CISPEP 11 PRO A 118 PRO A 119 11 1.60 CISPEP 12 PRO A 118 PRO A 119 12 -2.24 CISPEP 13 PRO A 118 PRO A 119 13 3.77 CISPEP 14 PRO A 118 PRO A 119 14 5.70 CISPEP 15 PRO A 118 PRO A 119 15 4.23 CISPEP 16 PRO A 118 PRO A 119 16 3.67 CISPEP 17 PRO A 118 PRO A 119 17 1.40 CISPEP 18 PRO A 118 PRO A 119 18 3.05 CISPEP 19 PRO A 118 PRO A 119 19 1.38 CISPEP 20 PRO A 118 PRO A 119 20 -3.23 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