HEADER HYDROLASE 01-OCT-10 2L47 TITLE SOLUTION STRUCTURE OF THE PLYG CATALYTIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLMURAMOYL-L-ALANINE AMIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 1-165; COMPND 5 EC: 3.5.1.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE GAMMA; SOURCE 3 ORGANISM_TAXID: 347962; SOURCE 4 GENE: PLYG, GAMMALSU_0017, GAMMAUSAM_0017; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL1 BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAD18 KEYWDS BACILLUS ANTHRACIS GAMMA-PHAGE ENDOLYSIN, PLYG, AMIDASE-2 FAMILY, ZN- KEYWDS 2 DEPENDENT PEPTIDOGLYCAN AMIDASE, CATALYTIC DOMAIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.F.VOLKMAN,J.S.DIAS,F.C.PETERSON REVDAT 1 12-OCT-11 2L47 0 JRNL AUTH J.S.DIAS,F.C.PETERSON,B.F.VOLKMAN JRNL TITL TBD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.3 REMARK 3 AUTHORS : SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE, REMARK 3 G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF 3503 REMARK 3 NOE CONSTRAINTS (634 INTRA, 594 SEQUENTIAL, 750 MEDIUM AND 1525 REMARK 3 LONG RANGE CONSTRAINTS) AND 216 PHI AND PSI DIHEDRAL ANGLE REMARK 3 CONSTRAINTS. REMARK 4 REMARK 4 2L47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-10. REMARK 100 THE RCSB ID CODE IS RCSB101935. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 13 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 PLYG, 10 MM [U-99% 2H] BIS-TRIS, REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY (AROMATIC) 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 2.1, NMRPIPE 2007, XEASY REMARK 210 1.3, GARANT 2.1, CYANA 2.1 REMARK 210 METHOD USED : AUTOMATED METHODS WERE USED FOR REMARK 210 BACKBONE CHEMICAL SHIFT REMARK 210 ASSIGNMENT AND ITERATIVE NOE REMARK 210 REFINEMENT. FINAL STRUCTURES WERE REMARK 210 OBTAINED BY MOLECULAR DYNAMICS IN REMARK 210 EXPLICIT SOLVENT 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: 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 OD1 ASP A 99 HZ3 LYS A 103 1.56 REMARK 500 OD2 ASP A 77 H SER A 81 1.57 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 LEU A 7 151.36 -42.33 REMARK 500 1 THR A 15 -26.12 -144.87 REMARK 500 1 CYS A 17 77.79 -151.29 REMARK 500 1 SER A 81 -70.35 -137.96 REMARK 500 1 ASN A 120 67.14 61.65 REMARK 500 1 SER A 133 -53.33 -122.16 REMARK 500 1 ASN A 158 -67.44 80.25 REMARK 500 1 THR A 162 -11.14 -155.76 REMARK 500 2 LYS A 6 42.53 -140.28 REMARK 500 2 LEU A 7 158.44 -47.87 REMARK 500 2 HIS A 54 -60.09 -97.99 REMARK 500 2 LYS A 60 -63.87 -103.26 REMARK 500 2 SER A 81 -64.56 -141.30 REMARK 500 2 ASN A 120 70.27 62.48 REMARK 500 2 TRP A 132 -60.14 -96.86 REMARK 500 2 ASN A 158 -50.87 75.78 REMARK 500 2 VAL A 159 5.15 -67.80 REMARK 500 2 THR A 161 -104.27 46.13 REMARK 500 2 THR A 162 -49.31 69.26 REMARK 500 3 LEU A 7 157.21 -45.59 REMARK 500 3 CYS A 17 67.90 -152.15 REMARK 500 3 ASN A 47 -70.78 -67.69 REMARK 500 3 ASN A 48 19.28 80.31 REMARK 500 3 HIS A 54 -62.50 -90.91 REMARK 500 3 SER A 81 -58.22 -147.23 REMARK 500 3 GLN A 85 -152.54 -127.11 REMARK 500 3 SER A 86 144.84 76.07 REMARK 500 3 ASN A 120 69.21 60.26 REMARK 500 3 TRP A 132 -60.08 -94.43 REMARK 500 3 ASN A 158 -37.18 164.56 REMARK 500 3 THR A 162 31.60 -82.24 REMARK 500 4 LEU A 7 150.76 -49.93 REMARK 500 4 CYS A 17 73.54 -153.65 REMARK 500 4 ASN A 49 -75.09 -92.77 REMARK 500 4 GLU A 50 -55.13 -142.76 REMARK 500 4 LYS A 60 -60.83 -99.11 REMARK 500 4 SER A 81 -68.80 -150.57 REMARK 500 4 ASN A 120 68.82 63.11 REMARK 500 4 SER A 133 -55.24 -122.06 REMARK 500 4 ASN A 158 -62.12 80.17 REMARK 500 5 LYS A 6 43.57 -147.82 REMARK 500 5 LEU A 7 166.32 -47.87 REMARK 500 5 PRO A 10 -19.51 -49.29 REMARK 500 5 TYR A 13 13.46 -63.71 REMARK 500 5 ASN A 47 -79.40 -65.35 REMARK 500 5 ASN A 48 68.21 70.04 REMARK 500 5 ASN A 49 -82.81 -140.44 REMARK 500 5 GLU A 50 -64.71 -139.61 REMARK 500 5 HIS A 54 -63.49 -91.75 REMARK 500 5 LYS A 60 -62.75 -105.85 REMARK 500 REMARK 500 THIS ENTRY HAS 187 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 8 ARG A 84 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 18 ASN A 48 24.9 L L OUTSIDE RANGE 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 1 ZN A 166 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 129 ND1 REMARK 620 2 HIS A 29 ND1 109.2 REMARK 620 3 CYS A 137 SG 106.4 115.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 166 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L48 RELATED DB: PDB DBREF 2L47 A 1 165 UNP Q8LTE6 Q8LTE6_9CAUD 1 165 SEQRES 1 A 165 MET GLU ILE GLN LYS LYS LEU VAL ASP PRO SER LYS TYR SEQRES 2 A 165 GLY THR LYS CYS PRO TYR THR MET LYS PRO LYS TYR ILE SEQRES 3 A 165 THR VAL HIS ASN THR TYR ASN ASP ALA PRO ALA GLU ASN SEQRES 4 A 165 GLU VAL SER TYR MET ILE SER ASN ASN ASN GLU VAL SER SEQRES 5 A 165 PHE HIS ILE ALA VAL ASP ASP LYS LYS ALA ILE GLN GLY SEQRES 6 A 165 ILE PRO LEU GLU ARG ASN ALA TRP ALA CYS GLY ASP GLY SEQRES 7 A 165 ASN GLY SER GLY ASN ARG GLN SER ILE SER VAL GLU ILE SEQRES 8 A 165 CYS TYR SER LYS SER GLY GLY ASP ARG TYR TYR LYS ALA SEQRES 9 A 165 GLU ASP ASN ALA VAL ASP VAL VAL ARG GLN LEU MET SER SEQRES 10 A 165 MET TYR ASN ILE PRO ILE GLU ASN VAL ARG THR HIS GLN SEQRES 11 A 165 SER TRP SER GLY LYS TYR CYS PRO HIS ARG MET LEU ALA SEQRES 12 A 165 GLU GLY ARG TRP GLY ALA PHE ILE GLN LYS VAL LYS ASN SEQRES 13 A 165 GLY ASN VAL ALA THR THR SER PRO THR HET ZN A 166 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 9 SER A 11 5 3 HELIX 2 2 LYS A 12 CYS A 17 1 6 HELIX 3 3 PRO A 36 ILE A 45 1 10 HELIX 4 4 SER A 81 GLN A 85 1 5 HELIX 5 5 GLY A 98 ASN A 120 1 23 HELIX 6 6 PRO A 122 GLU A 124 5 3 HELIX 7 7 PRO A 138 GLU A 144 1 7 HELIX 8 8 ARG A 146 GLY A 157 1 12 SHEET 1 A 6 ILE A 3 LYS A 5 0 SHEET 2 A 6 ALA A 62 GLN A 64 1 O GLN A 64 N GLN A 4 SHEET 3 A 6 ILE A 55 VAL A 57 -1 N ALA A 56 O ILE A 63 SHEET 4 A 6 SER A 86 ILE A 91 1 O GLU A 90 N VAL A 57 SHEET 5 A 6 TYR A 25 ASN A 30 1 N THR A 27 O ILE A 87 SHEET 6 A 6 VAL A 126 THR A 128 1 O ARG A 127 N ILE A 26 LINK ND1 HIS A 129 ZN ZN A 166 1555 1555 2.01 LINK ND1 HIS A 29 ZN ZN A 166 1555 1555 2.06 LINK SG CYS A 137 ZN ZN A 166 1555 1555 2.32 SITE 1 AC1 3 HIS A 29 HIS A 129 CYS A 137 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 211 0 1 8 6 0 1 6 0 0 0 13 END