HEADER HYDROLASE 07-JAN-05 2BH7 TITLE CRYSTAL STRUCTURE OF A SEMET DERIVATIVE OF AMID AT 2.2 TITLE 2 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLMURAMOYL-L-ALANINE AMIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.28 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12 MG1655 KEYWDS ZINC AMIDASE, PGRP, T7 LYSOZYME, AMPD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PETRELLA,R.HERMAN,E.SAUVAGE,C.GENEREUX,A.PENNARTZ,B.JORIS, AUTHOR 2 P.CHARLIER REVDAT 4 09-MAR-10 2BH7 1 JRNL REMARK REVDAT 3 02-FEB-10 2BH7 1 VERSN REVDAT 2 24-FEB-09 2BH7 1 VERSN REVDAT 1 22-JUN-06 2BH7 0 JRNL AUTH F.KERFF,S.PETRELLA,F.MERCIER,E.SAUVAGE,R.HERMAN, JRNL AUTH 2 A.PENNARTZ,A.ZERVOSEN,A.LUXEN,J.M.FRERE,B.JORIS, JRNL AUTH 3 P.CHARLIER JRNL TITL SPECIFIC STRUCTURAL FEATURES OF THE JRNL TITL 2 N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID FROM JRNL TITL 3 ESCHERICHIA COLI AND MECHANISTIC IMPLICATIONS FOR JRNL TITL 4 ENZYMES OF THIS FAMILY. JRNL REF J.MOL.BIOL. V. 397 249 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20036252 JRNL DOI 10.1016/J.JMB.2009.12.038 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2131583.74 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 21818 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.9 REMARK 3 FREE R VALUE TEST SET COUNT : 2167 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.3 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2838 REMARK 3 BIN R VALUE (WORKING SET) : 0.311 REMARK 3 BIN FREE R VALUE : 0.337 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.5 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 332 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2029 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.9 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.06 REMARK 3 B22 (A**2) : 5.06 REMARK 3 B33 (A**2) : -10.12 REMARK 3 B12 (A**2) : 4.48 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.36 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.2 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.1 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.85 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.38 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.38 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.09 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.23 ; 2.50 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.388993 REMARK 3 BSOL : 62.3704 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BH7 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JAN-05. REMARK 100 THE PDBE ID CODE IS EBI-22315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22663 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 48.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 57.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 23.10 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.4 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M MGSO4 ACETATE PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.30767 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 122.61533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.96150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 153.26917 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.65383 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.30767 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 122.61533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 153.26917 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 91.96150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 30.65383 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -246.4 KCAL/MOL 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 44.49500 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 77.06760 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 153.26917 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A 1 REMARK 465 GLY A 2 REMARK 465 ALA A 3 REMARK 465 GLY A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 465 ASP A 261 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2043 O HOH A 2043 10665 1.10 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 TYR A 14 168.24 178.03 REMARK 500 GLN A 52 -43.22 -167.35 REMARK 500 LYS A 117 98.92 -60.67 REMARK 500 ALA A 155 60.00 -152.26 REMARK 500 GLN A 173 -3.65 -59.55 REMARK 500 PRO A 180 -177.62 -56.18 REMARK 500 PRO A 216 46.66 -75.15 REMARK 500 ASP A 217 39.85 176.64 REMARK 500 ARG A 235 55.17 -145.49 REMARK 500 LEU A 238 118.17 -163.98 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 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 ND1 REMARK 620 2 ASP A 161 OD1 107.1 REMARK 620 3 HOH A2145 O 122.3 120.6 REMARK 620 4 HIS A 151 ND1 91.8 109.5 100.3 REMARK 620 N 1 2 3 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BGX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NATIVE AMID AT 1.8 ANGSTROM REMARK 900 RELATED ID: 2WKX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE NATIVE E. COLI REMARK 900 ZINC AMIDASE AMID REMARK 900 RELATED ID: 3D2Y RELATED DB: PDB REMARK 900 COMPLEX OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID REMARK 900 FROM E.COLI WITH THE SUBSTRATE ANHYDRO-N-ACETYLMURAMIC REMARK 900 ACID-L-ALA-D-GAMMA-GLU-L-LYS REMARK 900 RELATED ID: 3D2Z RELATED DB: PDB REMARK 900 COMPLEX OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE REMARK 900 AMID FROM E.COLI WITH THE PRODUCT L-ALA-D-GAMMA-GLU-L-LYS REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1 TO 17 WERE REMOVED AND A METHIONINE AND A REMARK 999 GLYCINE WERE ADDED AT THE BEGINNING OF THE PROTEIN DBREF 2BH7 A 1 2 PDB 2BH7 2BH7 1 2 DBREF 2BH7 A 3 261 UNP P75820 YBJR_ECOLI 18 276 SEQRES 1 A 261 MSE GLY ALA GLY GLU LYS GLY ILE VAL GLU LYS GLU GLY SEQRES 2 A 261 TYR GLN LEU ASP THR ARG ARG GLN ALA GLN ALA ALA TYR SEQRES 3 A 261 PRO ARG ILE LYS VAL LEU VAL ILE HIS TYR THR ALA ASP SEQRES 4 A 261 ASP PHE ASP SER SER LEU ALA THR LEU THR ASP LYS GLN SEQRES 5 A 261 VAL SER SER HIS TYR LEU VAL PRO ALA VAL PRO PRO ARG SEQRES 6 A 261 TYR ASN GLY LYS PRO ARG ILE TRP GLN LEU VAL PRO GLU SEQRES 7 A 261 GLN GLU LEU ALA TRP HIS ALA GLY ILE SER ALA TRP ARG SEQRES 8 A 261 GLY ALA THR ARG LEU ASN ASP THR SER ILE GLY ILE GLU SEQRES 9 A 261 LEU GLU ASN ARG GLY TRP GLN LYS SER ALA GLY VAL LYS SEQRES 10 A 261 TYR PHE ALA PRO PHE GLU PRO ALA GLN ILE GLN ALA LEU SEQRES 11 A 261 ILE PRO LEU ALA LYS ASP ILE ILE ALA ARG TYR HIS ILE SEQRES 12 A 261 LYS PRO GLU ASN VAL VAL ALA HIS ALA ASP ILE ALA PRO SEQRES 13 A 261 GLN ARG LYS ASP ASP PRO GLY PRO LEU PHE PRO TRP GLN SEQRES 14 A 261 GLN LEU ALA GLN GLN GLY ILE GLY ALA TRP PRO ASP ALA SEQRES 15 A 261 GLN ARG VAL ASN PHE TYR LEU ALA GLY ARG ALA PRO HIS SEQRES 16 A 261 THR PRO VAL ASP THR ALA SER LEU LEU GLU LEU LEU ALA SEQRES 17 A 261 ARG TYR GLY TYR ASP VAL LYS PRO ASP MSE THR PRO ARG SEQRES 18 A 261 GLU GLN ARG ARG VAL ILE MSE ALA PHE GLN MSE HIS PHE SEQRES 19 A 261 ARG PRO THR LEU TYR ASN GLY GLU ALA ASP ALA GLU THR SEQRES 20 A 261 GLN ALA ILE ALA GLU ALA LEU LEU GLU LYS TYR GLY GLN SEQRES 21 A 261 ASP MODRES 2BH7 MSE A 218 MET SELENOMETHIONINE MODRES 2BH7 MSE A 228 MET SELENOMETHIONINE MODRES 2BH7 MSE A 232 MET SELENOMETHIONINE HET MSE A 218 8 HET MSE A 228 8 HET MSE A 232 8 HET ZN A 300 1 HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HET SO4 A 305 5 HET SO4 A 306 5 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 6(O4 S 2-) FORMUL 4 HOH *147(H2 O) HELIX 1 1 ASP A 40 LEU A 48 1 9 HELIX 2 2 GLU A 123 TYR A 141 1 19 HELIX 3 3 LYS A 144 GLU A 146 5 3 HELIX 4 4 HIS A 151 ALA A 155 1 5 HELIX 5 5 PRO A 167 GLN A 173 1 7 HELIX 6 6 ASP A 181 ALA A 190 1 10 HELIX 7 7 ASP A 199 GLY A 211 1 13 HELIX 8 8 THR A 219 ARG A 235 1 17 HELIX 9 9 ASP A 244 GLY A 259 1 16 SHEET 1 AA 2 ILE A 8 LYS A 11 0 SHEET 2 AA 2 TYR A 14 ASP A 17 -1 O TYR A 14 N LYS A 11 SHEET 1 AB 5 TRP A 73 GLN A 74 0 SHEET 2 AB 5 TYR A 57 VAL A 59 -1 O LEU A 58 N TRP A 73 SHEET 3 AB 5 SER A 100 LEU A 105 1 O GLU A 104 N VAL A 59 SHEET 4 AB 5 VAL A 31 TYR A 36 1 O VAL A 31 N ILE A 101 SHEET 5 AB 5 VAL A 148 ALA A 150 1 O VAL A 149 N ILE A 34 SHEET 1 AC 2 ARG A 65 TYR A 66 0 SHEET 2 AC 2 LYS A 69 PRO A 70 -1 O LYS A 69 N TYR A 66 SHEET 1 AD 2 ALA A 89 TRP A 90 0 SHEET 2 AD 2 ALA A 93 THR A 94 -1 O ALA A 93 N TRP A 90 SHEET 1 AE 2 TRP A 110 SER A 113 0 SHEET 2 AE 2 VAL A 116 PHE A 119 -1 O VAL A 116 N SER A 113 LINK C ASP A 217 N MSE A 218 1555 1555 1.33 LINK C MSE A 218 N THR A 219 1555 1555 1.32 LINK C ILE A 227 N MSE A 228 1555 1555 1.32 LINK C MSE A 228 N ALA A 229 1555 1555 1.33 LINK C GLN A 231 N MSE A 232 1555 1555 1.33 LINK C MSE A 232 N HIS A 233 1555 1555 1.33 LINK ZN ZN A 300 ND1 HIS A 35 1555 1555 2.48 LINK ZN ZN A 300 OD1 ASP A 161 1555 1555 2.16 LINK ZN ZN A 300 O HOH A2145 1555 1555 2.05 LINK ZN ZN A 300 ND1 HIS A 151 1555 1555 2.21 CISPEP 1 ASP A 161 PRO A 162 0 0.31 SITE 1 AC1 4 HIS A 35 HIS A 151 ASP A 161 HOH A2145 SITE 1 AC2 3 ILE A 87 ARG A 95 HOH A2045 SITE 1 AC3 4 ASP A 17 ARG A 19 ARG A 20 TRP A 73 SITE 1 AC4 5 TYR A 36 TRP A 110 LYS A 159 ASP A 160 SITE 2 AC4 5 ASP A 161 SITE 1 AC5 4 ARG A 108 GLN A 111 VAL A 198 ASP A 199 SITE 1 AC6 4 ARG A 91 LYS A 144 GLU A 146 ASN A 147 SITE 1 AC7 5 ALA A 85 GLY A 86 HIS A 151 ARG A 158 SITE 2 AC7 5 LYS A 159 CRYST1 88.990 88.990 183.923 90.00 90.00 120.00 P 61 2 2 12 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 0.011237 0.006488 0.000000 0.00000 SCALE2 0.000000 0.012976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005437 0.00000