HEADER TRANSFERASE 09-JUN-11 3ZQD TITLE B. SUBTILIS L,D-TRANSPEPTIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: L, D-TRANSPEPTIDASE YKUD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPORE PROTEIN YKUD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 ATCC: 168; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PREP4GROESL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET2818 KEYWDS TRANSFERASE, PEPTIDOGLYCAN, ANTIBIOTIC RESISTANCE, CYSTEINE PROTEASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.LECOQ,J.-P.SIMORRE,C.BOUGAULT,M.ARTHUR,J.-E.HUGONNET,C.VECKERLE, AUTHOR 2 O.PESSEY REVDAT 3 14-JUN-23 3ZQD 1 REMARK ATOM REVDAT 2 24-JAN-18 3ZQD 1 JRNL REMARK REVDAT 1 23-MAY-12 3ZQD 0 JRNL AUTH L.LECOQ,C.BOUGAULT,J.HUGONNET,C.VECKERLE,O.PESSEY,M.ARTHUR, JRNL AUTH 2 J.SIMORRE JRNL TITL DYNAMICS INDUCED BY BETA-LACTAM ANTIBIOTICS IN THE ACTIVE JRNL TITL 2 SITE OF BACILLUS SUBTILIS L,D-TRANSPEPTIDASE. JRNL REF STRUCTURE V. 20 850 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22579252 JRNL DOI 10.1016/J.STR.2012.03.015 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.BIELNICKI,Y.DEVEDJIEV,U.DEREWENDA,Z.DAUTER,A.JOACHIMIAK, REMARK 1 AUTH 2 Z.S.DEREWENDA REMARK 1 TITL B. SUBTILIS YKUD PROTEIN AT 2.0 A RESOLUTION: INSIGHTS INTO REMARK 1 TITL 2 THE STRUCTURE AND FUNCTION OF A NOVEL, UBIQUITOUS FAMILY OF REMARK 1 TITL 3 BACTERIAL ENZYMES. REMARK 1 REF PROTEINS V. 62 144 2006 REMARK 1 REFN ISSN 0887-3585 REMARK 1 PMID 16287140 REMARK 1 DOI 10.1002/PROT.20702 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, READ,RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 3ZQD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1290048629. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : [1H; 15N]-HSQC; 13C]-NOESY-HSQ REMARK 210 IN THE ALIPHATIC REGION; HNCACB; REMARK 210 HNCO; 13C]-HSQC IN THE ALIPHATIC REMARK 210 REGION; METHYL SELECTIVE [1H; REMARK 210 13C] -HSQC-NOESY; 13C]-HSQC IN REMARK 210 THE AROMATIC REGION; 15N] SOFAST- REMARK 210 HMQC ON THE HISTIDINES; [1H-15N]- REMARK 210 NOESY- HSQC; 13C]- NOESY-HSQC IN REMARK 210 THE AROMATIC REGION REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, NMRPIPE, CCPNMR REMARK 210 ANALYSIS 2.1 REMARK 210 METHOD USED : ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY AND N-H AND CA-HA RDCS ON 13C, 15N-LABELED LDTBS. REMARK 210 THE 20 STRUCTURES OF MINIMAL ENERGY WERE FURTHER REFINED IN REMARK 210 WATER. 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 400 REMARK 400 COMPOUND REMARK 400 HIS 126 IS PROTONATED ON THE ND1 (ND1=ATOM 1950 AND HD1=ATOM 1958) REMARK 400 AND NON PROTONATED ON THE NE2 (ATOM 1953). CYS 142 IS PROTONATED REMARK 400 ON THE SG (SG=ATOM 2164 AND HG=ATOM 2169). 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 1-20 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 SER A 169 O 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 6 PHE A 111 CE1 PHE A 111 CZ 0.123 REMARK 500 7 PHE A 111 CE1 PHE A 111 CZ 0.125 REMARK 500 10 TYR A 99 CZ TYR A 99 CE2 -0.085 REMARK 500 14 PHE A 111 CE1 PHE A 111 CZ 0.124 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 ILE A 24 -165.53 -120.53 REMARK 500 1 ASN A 76 -13.19 74.76 REMARK 500 1 LYS A 88 2.68 -56.37 REMARK 500 1 ASN A 102 179.18 178.82 REMARK 500 1 ASN A 106 102.97 -34.75 REMARK 500 1 PRO A 110 5.16 -59.69 REMARK 500 1 ALA A 113 -2.20 39.31 REMARK 500 1 TYR A 123 38.16 -91.31 REMARK 500 1 LYS A 140 -43.32 -132.56 REMARK 500 1 ILE A 143 98.03 -59.90 REMARK 500 1 GLU A 152 -72.71 -45.09 REMARK 500 2 GLN A 11 107.68 -58.23 REMARK 500 2 ASP A 13 170.16 -54.46 REMARK 500 2 ILE A 24 -165.52 -114.30 REMARK 500 2 ASN A 76 -10.03 71.90 REMARK 500 2 LYS A 88 2.70 -57.71 REMARK 500 2 ASN A 102 177.79 179.97 REMARK 500 2 ASN A 106 102.33 -34.86 REMARK 500 2 PRO A 110 5.36 -61.60 REMARK 500 2 ALA A 113 0.31 37.75 REMARK 500 2 TYR A 123 37.42 -94.80 REMARK 500 2 LYS A 140 -44.59 -131.17 REMARK 500 2 ILE A 143 96.83 -59.75 REMARK 500 2 MET A 145 -164.82 -126.45 REMARK 500 3 ILE A 24 -165.78 -116.78 REMARK 500 3 PRO A 34 -9.94 -58.24 REMARK 500 3 ASN A 75 68.07 30.97 REMARK 500 3 ASN A 76 -9.41 72.09 REMARK 500 3 LYS A 88 3.60 -57.13 REMARK 500 3 ASN A 106 104.90 -35.27 REMARK 500 3 PRO A 110 2.42 -59.52 REMARK 500 3 PHE A 111 16.08 -69.84 REMARK 500 3 ALA A 113 -3.90 39.38 REMARK 500 3 TYR A 123 37.50 -96.33 REMARK 500 3 LYS A 140 -45.57 -131.93 REMARK 500 3 ILE A 143 97.48 -59.87 REMARK 500 3 GLU A 152 -71.83 -46.84 REMARK 500 4 ILE A 24 -165.25 -118.34 REMARK 500 4 ASN A 76 -13.89 78.15 REMARK 500 4 LYS A 88 4.63 -57.27 REMARK 500 4 ASN A 102 176.05 177.99 REMARK 500 4 ASN A 106 101.08 -36.10 REMARK 500 4 ALA A 113 -54.23 173.92 REMARK 500 4 TYR A 123 38.19 -97.21 REMARK 500 4 LYS A 140 -43.99 -133.52 REMARK 500 4 ILE A 143 97.36 -60.61 REMARK 500 4 MET A 145 -169.00 -121.38 REMARK 500 4 GLU A 152 -70.87 -45.12 REMARK 500 5 ILE A 24 -165.50 -113.87 REMARK 500 5 PRO A 34 -4.41 -59.50 REMARK 500 REMARK 500 THIS ENTRY HAS 233 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 105 ASN A 106 11 -147.60 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 4 ARG A 103 0.08 SIDE CHAIN REMARK 500 5 ARG A 103 0.08 SIDE CHAIN REMARK 500 9 ARG A 103 0.10 SIDE CHAIN REMARK 500 11 ARG A 103 0.08 SIDE CHAIN REMARK 500 12 ARG A 103 0.09 SIDE CHAIN REMARK 500 18 ARG A 103 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y7M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE B. SUBTILIS YKUD PROTEIN AT 2 ARESOLUTION REMARK 900 RELATED ID: 17701 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 GENE SEQUENCING LED TO THE REPLACEMENT OF THE FIRST MET BY REMARK 999 GRKL, AND TO THE ADDITION OF THE C-TERMINAL HIS-TAG REMARK 999 GSHHHHHH DBREF 3ZQD A 5 167 UNP O34816 YKUD_BACSU 2 164 SEQADV 3ZQD GLY A 1 UNP O34816 EXPRESSION TAG SEQADV 3ZQD ARG A 2 UNP O34816 EXPRESSION TAG SEQADV 3ZQD LYS A 3 UNP O34816 EXPRESSION TAG SEQADV 3ZQD LEU A 4 UNP O34816 EXPRESSION TAG SEQADV 3ZQD GLY A 168 UNP O34816 EXPRESSION TAG SEQADV 3ZQD SER A 169 UNP O34816 EXPRESSION TAG SEQADV 3ZQD HIS A 170 UNP O34816 EXPRESSION TAG SEQADV 3ZQD HIS A 171 UNP O34816 EXPRESSION TAG SEQADV 3ZQD HIS A 172 UNP O34816 EXPRESSION TAG SEQADV 3ZQD HIS A 173 UNP O34816 EXPRESSION TAG SEQADV 3ZQD HIS A 174 UNP O34816 EXPRESSION TAG SEQADV 3ZQD 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 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 PRO A 34 GLY A 39 1 6 HELIX 4 4 ASN A 130 ILE A 134 5 5 HELIX 5 5 HIS A 146 VAL A 157 1 12 SHEET 1 AA 2 LEU A 4 GLN A 8 0 SHEET 2 AA 2 SER A 45 PRO A 52 -1 O ILE A 46 N TYR A 7 SHEET 1 AB 7 ARG A 77 PRO A 83 0 SHEET 2 AB 7 THR A 69 LEU A 74 -1 O LEU A 70 N TYR A 82 SHEET 3 AB 7 TYR A 59 SER A 64 -1 O HIS A 60 N SER A 73 SHEET 4 AB 7 ARG A 162 ASN A 166 1 O ARG A 162 N ILE A 61 SHEET 5 AB 7 GLU A 97 ARG A 105 -1 O PHE A 98 N VAL A 163 SHEET 6 AB 7 TYR A 114 LEU A 118 -1 O TRP A 115 N GLN A 104 SHEET 7 AB 7 ILE A 125 HIS A 126 -1 O ILE A 125 N LEU A 116 SHEET 1 AC 2 VAL A 86 GLY A 87 0 SHEET 2 AC 2 ALA A 137 VAL A 138 1 N VAL A 138 O VAL A 86 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