HEADER TRANSFERASE/STRUCTURAL PROTEIN 02-SEP-14 2MTZ TITLE HADDOCK MODEL OF BACILLUS SUBTILIS L,D-TRANSPEPTIDASE IN COMPLEX WITH TITLE 2 A PEPTIDOGLYCAN HEXAMUROPEPTIDE CAVEAT 2MTZ NAG H 4 HAS WRONG CHIRALITY AT ATOM C1 NAG H 8 HAS WRONG CAVEAT 2 2MTZ CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE L,D-TRANSPEPTIDASE YKUD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-167; COMPND 5 SYNONYM: SPORE PROTEIN YKUD; COMPND 6 EC: 2.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: INTACT BACTERIAL PEPTIDOGLYCAN; COMPND 10 CHAIN: B, C, D, E, F, G SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: BSU14040, Y647_14120, YKUD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET2818; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 13 ORGANISM_TAXID: 1423 KEYWDS TRANSPEPTIDASE, PEPTIDOGLYCAN BIOSYNTHESIS, TRANSFERASE-STRUCTURAL KEYWDS 2 PROTEIN COMPLEX EXPDTA SOLID-STATE NMR NUMMDL 5 AUTHOR P.SCHANDA,S.TRIBOULET,C.LAGURI,C.BOUGAULT,I.AYALA,M.CALLON,M.ARTHUR, AUTHOR 2 J.SIMORRE REVDAT 3 15-NOV-23 2MTZ 1 HETSYN LINK ATOM REVDAT 2 29-JUL-20 2MTZ 1 CAVEAT COMPND REMARK SEQADV REVDAT 2 2 1 HETNAM LINK SITE ATOM REVDAT 1 14-JAN-15 2MTZ 0 JRNL AUTH P.SCHANDA,S.TRIBOULET,C.LAGURI,C.M.BOUGAULT,I.AYALA, JRNL AUTH 2 M.CALLON,M.ARTHUR,J.P.SIMORRE JRNL TITL ATOMIC MODEL OF A CELL-WALL CROSS-LINKING ENZYME IN COMPLEX JRNL TITL 2 WITH AN INTACT BACTERIAL PEPTIDOGLYCAN. JRNL REF J.AM.CHEM.SOC. V. 136 17852 2014 JRNL REFN ISSN 0002-7863 JRNL PMID 25429710 JRNL DOI 10.1021/JA5105987 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 2.1, HADDOCK 2.1 REMARK 3 AUTHORS : ALEXANDRE BONVIN (HADDOCK), ALEXANDRE BONVIN REMARK 3 (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK STARTING STRUCTURE FOR CHAIN A REMARK 3 IS PDB ENTRY 3ZQD. THE PEPTIDOGLYCAN LIGAND STARTING STRUCTURE REMARK 3 WAS GENERATED BY CNS. REMARK 4 REMARK 4 2MTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000104042. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.5 MG/ML [U-13C; U-15N; U-2H] REMARK 210 PROTEIN, 3 MG/ML PEPTIDE, 50 MM REMARK 210 HEPES; 376 UM [U-99% 13C; U-99% REMARK 210 15N] PROTEIN, 50 MM HEPES REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C-13C DARR; HCANH; HNH; 3D REMARK 210 HNCA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 1000 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : AGILENT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 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 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 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: HEPTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 400 REMARK 400 COMPOUND REMARK 400 THIS STRUCTURE CONTAINS A PEPTIDOGLYCAN LIGAND COMPOSED OF SIX REMARK 400 TETRAPEPTIDES (CHAIN B, C, D, E, F, AND G) AND ONE POLYSACCHARIDE REMARK 400 (CHAIN E) COVALENTLY LINKED TOGETHER AS ONE ENTITY. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-5 REMARK 465 RES C SSSEQI REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 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 10 -168.39 -123.95 REMARK 500 1 PRO A 58 26.74 -79.69 REMARK 500 1 ASN A 106 86.67 52.48 REMARK 500 1 ALA A 113 -53.33 70.77 REMARK 500 1 SER A 139 -78.28 -57.18 REMARK 500 1 PRO A 158 -142.21 -94.45 REMARK 500 2 ASN A 106 89.40 53.74 REMARK 500 2 ALA A 113 -9.90 71.97 REMARK 500 2 GLN A 121 -75.11 -59.13 REMARK 500 2 HIS A 122 26.36 -77.62 REMARK 500 2 SER A 139 -78.88 -68.66 REMARK 500 3 ALA A 67 -38.08 -160.54 REMARK 500 3 ASN A 76 -14.13 86.93 REMARK 500 3 MET A 79 -66.79 -109.91 REMARK 500 3 ASN A 106 89.29 61.03 REMARK 500 3 ALA A 113 -42.45 71.41 REMARK 500 3 SER A 139 -81.83 -65.55 REMARK 500 3 PRO A 158 -157.17 -88.51 REMARK 500 4 ARG A 2 99.43 -67.27 REMARK 500 4 LYS A 10 -81.29 -94.35 REMARK 500 4 GLN A 11 137.54 -174.60 REMARK 500 4 ASN A 76 -1.92 81.90 REMARK 500 4 THR A 95 162.42 174.01 REMARK 500 4 ASN A 106 78.86 48.28 REMARK 500 4 PRO A 110 48.25 -78.35 REMARK 500 4 GLN A 121 -74.42 -48.46 REMARK 500 4 SER A 139 -84.55 -72.58 REMARK 500 4 THR A 164 97.83 -68.25 REMARK 500 5 LYS A 3 93.04 -68.45 REMARK 500 5 ASN A 76 -1.45 91.63 REMARK 500 5 MET A 79 -63.72 -108.74 REMARK 500 5 ASN A 106 85.30 56.11 REMARK 500 5 ALA A 113 -27.63 71.02 REMARK 500 5 SER A 119 27.91 -79.06 REMARK 500 5 LYS A 120 125.74 -170.20 REMARK 500 5 SER A 139 -80.16 -55.38 REMARK 500 5 PRO A 158 -157.23 -86.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18037 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE IMIPENEM-ACYLATED L,D-TRANSPEPTIDASE FROM REMARK 900 BACILLUS SUBTILIS REMARK 900 RELATED ID: 25192 RELATED DB: BMRB REMARK 900 RELATED ID: 3ZQD RELATED DB: PDB REMARK 900 HADDOCK STARTING STRUCTURE DBREF 2MTZ A 5 167 UNP O34816 YKUD_BACSU 2 164 DBREF 2MTZ B 3 6 PDB 2MTZ 2MTZ 3 6 DBREF 2MTZ C 9 12 PDB 2MTZ 2MTZ 9 12 DBREF 2MTZ D 15 18 PDB 2MTZ 2MTZ 15 18 DBREF 2MTZ E 21 24 PDB 2MTZ 2MTZ 21 24 DBREF 2MTZ F 27 30 PDB 2MTZ 2MTZ 27 30 DBREF 2MTZ G 33 36 PDB 2MTZ 2MTZ 33 36 SEQADV 2MTZ GLY A 1 UNP O34816 EXPRESSION TAG SEQADV 2MTZ ARG A 2 UNP O34816 EXPRESSION TAG SEQADV 2MTZ LYS A 3 UNP O34816 EXPRESSION TAG SEQADV 2MTZ LEU A 4 UNP O34816 EXPRESSION TAG SEQADV 2MTZ GLY A 168 UNP O34816 EXPRESSION TAG SEQADV 2MTZ SER A 169 UNP O34816 EXPRESSION TAG SEQADV 2MTZ HIS A 170 UNP O34816 EXPRESSION TAG SEQADV 2MTZ HIS A 171 UNP O34816 EXPRESSION TAG SEQADV 2MTZ HIS A 172 UNP O34816 EXPRESSION TAG SEQADV 2MTZ HIS A 173 UNP O34816 EXPRESSION TAG SEQADV 2MTZ HIS A 174 UNP O34816 EXPRESSION TAG SEQADV 2MTZ HIS A 175 UNP O34816 EXPRESSION TAG SEQRES 1 A 175 GLY ARG LYS LEU LEU THR TYR GLN VAL LYS GLN GLY ASP SEQRES 2 A 175 THR LEU ASN SER ILE ALA ALA ASP PHE ARG ILE SER THR SEQRES 3 A 175 ALA ALA LEU LEU GLN ALA ASN PRO SER LEU GLN ALA GLY SEQRES 4 A 175 LEU THR ALA GLY GLN SER ILE VAL ILE PRO GLY LEU PRO SEQRES 5 A 175 ASP PRO TYR THR ILE PRO TYR HIS ILE ALA VAL SER ILE SEQRES 6 A 175 GLY ALA LYS THR LEU THR LEU SER LEU ASN ASN ARG VAL SEQRES 7 A 175 MET LYS THR TYR PRO ILE ALA VAL GLY LYS ILE LEU THR SEQRES 8 A 175 GLN THR PRO THR GLY GLU PHE TYR ILE ILE ASN ARG GLN SEQRES 9 A 175 ARG ASN PRO GLY GLY PRO PHE GLY ALA TYR TRP LEU SER SEQRES 10 A 175 LEU SER LYS GLN HIS TYR GLY ILE HIS GLY THR ASN ASN SEQRES 11 A 175 PRO ALA SER ILE GLY LYS ALA VAL SER LYS GLY CYS ILE SEQRES 12 A 175 ARG MET HIS ASN LYS ASP VAL ILE GLU LEU ALA SER ILE SEQRES 13 A 175 VAL PRO ASN GLY THR ARG VAL THR ILE ASN ARG GLY SER SEQRES 14 A 175 HIS HIS HIS HIS HIS HIS SEQRES 1 B 4 ALA FGA API DAL SEQRES 1 C 4 ALA FGA API DAL SEQRES 1 D 4 ALA FGA API DAL SEQRES 1 E 4 ALA FGA API DAL SEQRES 1 F 4 ALA FGA API DAL SEQRES 1 G 4 ALA FGA API DAL MODRES 2MTZ API B 5 LYS 2,6-DIAMINOPIMELIC ACID MODRES 2MTZ API C 11 LYS 2,6-DIAMINOPIMELIC ACID MODRES 2MTZ API D 17 LYS 2,6-DIAMINOPIMELIC ACID MODRES 2MTZ API E 23 LYS 2,6-DIAMINOPIMELIC ACID MODRES 2MTZ API F 29 LYS 2,6-DIAMINOPIMELIC ACID MODRES 2MTZ API G 35 LYS 2,6-DIAMINOPIMELIC ACID HET FGA B 4 9 HET API B 5 12 HET DAL B 6 6 HET FGA C 10 9 HET API C 11 12 HET DAL C 12 6 HET FGA D 16 9 HET API D 17 12 HET DAL D 18 6 HET FGA E 22 9 HET API E 23 12 HET DAL E 24 6 HET FGA F 28 9 HET API F 29 12 HET DAL F 30 6 HET FGA G 34 9 HET API G 35 12 HET DAL G 36 6 HET AMU H 1 19 HET NAG H 2 14 HET AMU H 3 18 HET NAG H 4 14 HET AMU H 5 18 HET NAG H 6 14 HET AMU H 7 18 HET NAG H 8 14 HET AMU H 9 18 HET NAG H 10 14 HET AMU H 11 18 HET NAG H 12 14 HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM API 2,6-DIAMINOPIMELIC ACID HETNAM DAL D-ALANINE HETNAM AMU N-ACETYL-BETA-MURAMIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN FGA D-GLUTAMIC ACID HETSYN AMU N-ACETYL-MURAMIC ACID; BETA-N-ACETYLMURAMIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 FGA 6(C5 H9 N O4) FORMUL 2 API 6(C7 H14 N2 O4) FORMUL 2 DAL 6(C3 H7 N O2) FORMUL 8 AMU 6(C11 H19 N O8) FORMUL 8 NAG 6(C8 H15 N O6) HELIX 1 1 THR A 14 PHE A 22 1 9 HELIX 2 2 SER A 25 ASN A 33 1 9 HELIX 3 3 ASN A 130 ILE A 134 5 5 HELIX 4 4 HIS A 146 VAL A 157 1 12 SHEET 1 A 2 LEU A 4 GLN A 8 0 SHEET 2 A 2 SER A 45 PRO A 52 -1 O ILE A 46 N TYR A 7 SHEET 1 B 5 ARG A 77 PRO A 83 0 SHEET 2 B 5 THR A 69 LEU A 74 -1 N LEU A 70 O TYR A 82 SHEET 3 B 5 TYR A 59 SER A 64 -1 N ALA A 62 O THR A 71 SHEET 4 B 5 ARG A 162 ASN A 166 1 O THR A 164 N ILE A 61 SHEET 5 B 5 GLU A 97 TYR A 99 -1 N PHE A 98 O VAL A 163 SHEET 1 C 2 VAL A 86 GLY A 87 0 SHEET 2 C 2 ALA A 137 VAL A 138 1 O VAL A 138 N VAL A 86 SHEET 1 D 4 ASN A 102 ARG A 105 0 SHEET 2 D 4 TYR A 114 SER A 117 -1 O TRP A 115 N GLN A 104 SHEET 3 D 4 ILE A 125 HIS A 126 -1 O ILE A 125 N LEU A 116 SHEET 4 D 4 ILE A 143 ARG A 144 1 O ILE A 143 N HIS A 126 LINK C ALA B 3 N FGA B 4 1555 1555 1.34 LINK N ALA B 3 C10 AMU H 11 1555 1555 1.34 LINK CD FGA B 4 N API B 5 1555 1555 1.34 LINK C API B 5 N DAL B 6 1555 1555 1.34 LINK C ALA C 9 N FGA C 10 1555 1555 1.34 LINK N ALA C 9 C10 AMU H 9 1555 1555 1.34 LINK CD FGA C 10 N API C 11 1555 1555 1.34 LINK C API C 11 N DAL C 12 1555 1555 1.34 LINK C ALA D 15 N FGA D 16 1555 1555 1.34 LINK N ALA D 15 C10 AMU H 7 1555 1555 1.34 LINK CD FGA D 16 N API D 17 1555 1555 1.34 LINK C API D 17 N DAL D 18 1555 1555 1.34 LINK C ALA E 21 N FGA E 22 1555 1555 1.34 LINK N ALA E 21 C10 AMU H 5 1555 1555 1.34 LINK CD FGA E 22 N API E 23 1555 1555 1.34 LINK C API E 23 N DAL E 24 1555 1555 1.34 LINK C ALA F 27 N FGA F 28 1555 1555 1.34 LINK N ALA F 27 C10 AMU H 3 1555 1555 1.34 LINK CD FGA F 28 N API F 29 1555 1555 1.34 LINK C API F 29 N DAL F 30 1555 1555 1.34 LINK C ALA G 33 N FGA G 34 1555 1555 1.34 LINK N ALA G 33 C10 AMU H 1 1555 1555 1.34 LINK CD FGA G 34 N API G 35 1555 1555 1.34 LINK C API G 35 N DAL G 36 1555 1555 1.34 LINK O4 AMU H 1 C1 NAG H 2 1555 1555 1.44 LINK O4 NAG H 2 C1 AMU H 3 1555 1555 1.44 LINK O4 AMU H 3 C1 NAG H 4 1555 1555 1.44 LINK O4 NAG H 4 C1 AMU H 5 1555 1555 1.44 LINK O4 AMU H 5 C1 NAG H 6 1555 1555 1.44 LINK O4 NAG H 6 C1 AMU H 7 1555 1555 1.44 LINK O4 AMU H 7 C1 NAG H 8 1555 1555 1.44 LINK O4 NAG H 8 C1 AMU H 9 1555 1555 1.43 LINK O4 AMU H 9 C1 NAG H 10 1555 1555 1.44 LINK O4 NAG H 10 C1 AMU H 11 1555 1555 1.44 LINK O4 AMU H 11 C1 NAG H 12 1555 1555 1.44 CISPEP 1 ALA D 15 FGA D 16 1 -0.10 CISPEP 2 ALA D 15 FGA D 16 2 0.10 CISPEP 3 ALA D 15 FGA D 16 3 0.00 CISPEP 4 ALA D 15 FGA D 16 4 0.03 CISPEP 5 ALA D 15 FGA D 16 5 0.07 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