HEADER HYDROLASE 09-MAY-08 3D2Z TITLE COMPLEX OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID FROM E.COLI WITH TITLE 2 THE PRODUCT L-ALA-D-GAMMA-GLU-L-LYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.28; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: L-ALA-D-GAMMA-GLU-L-LYS PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI STR. K12 SUBSTR. MG1655; SOURCE 3 ORGANISM_TAXID: 511145; SOURCE 4 STRAIN: K-12 MG1655; SOURCE 5 GENE: AMID, YBJR, B0867, JW0851; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: LMG194; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBAD/MYC-HISA; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED KEYWDS ZINC AMIDASE, PGRP, PEPTIDOGLYCAN RECOGNIZING PROTEIN, AMPD, N- KEYWDS 2 ACETYLMURAMYL-L-ALANINE AMIDASE, CELL WALL BIOGENESIS/DEGRADATION, KEYWDS 3 HYDROLASE, LIPOPROTEIN, MEMBRANE, METAL-BINDING, OUTER MEMBRANE, KEYWDS 4 PALMITATE EXPDTA X-RAY DIFFRACTION AUTHOR F.KERFF,S.PETRELLA,R.HERMAN,E.SAUVAGE,F.MERCIER,A.LUXEN,J.M.FRERE, AUTHOR 2 B.JORIS,P.CHARLIER REVDAT 5 30-AUG-23 3D2Z 1 REMARK SEQADV LINK REVDAT 4 27-JUL-11 3D2Z 1 HETNAM HETSYN REVDAT 3 13-JUL-11 3D2Z 1 VERSN REVDAT 2 16-MAR-10 3D2Z 1 JRNL REVDAT 1 16-JUN-09 3D2Z 0 JRNL AUTH F.KERFF,S.PETRELLA,F.MERCIER,E.SAUVAGE,R.HERMAN,A.PENNARTZ, JRNL AUTH 2 A.ZERVOSEN,A.LUXEN,J.M.FRERE,B.JORIS,P.CHARLIER JRNL TITL SPECIFIC STRUCTURAL FEATURES OF THE JRNL TITL 2 N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID FROM ESCHERICHIA JRNL TITL 3 COLI AND MECHANISTIC IMPLICATIONS FOR ENZYMES OF THIS JRNL TITL 4 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. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 10706 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 + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 551 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 775 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2071 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : -0.47000 REMARK 3 B12 (A**2) : 0.16000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.582 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.338 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.270 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.913 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.900 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.859 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2127 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2897 ; 1.356 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 256 ; 6.368 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;36.415 ;23.654 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 339 ;16.723 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.008 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 306 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1668 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 847 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1419 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 61 ; 0.173 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.084 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 46 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.151 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1343 ; 0.894 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2095 ; 1.537 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 910 ; 0.647 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 802 ; 1.069 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3D2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11312 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.40 REMARK 200 R MERGE (I) : 0.26300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 21.00 REMARK 200 R MERGE FOR SHELL (I) : 0.69800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2BGX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M LICL, 10 % PEG 6K, 0.1M ZNCL2, PH REMARK 280 4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 61.21333 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 122.42667 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 91.82000 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 153.03333 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 30.60667 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 61.21333 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 122.42667 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 153.03333 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 91.82000 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 30.60667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER BUT THE PROTEIN IS REMARK 300 FOUND AS A DIMER IN THE CRYSTAL WITH A SWAPPING OF THE N-TERMINUS 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: 900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -171.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -1.000000 0.000000 0.000000 -89.16000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 91.82000 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 ALA A 3 REMARK 465 GLY A 4 REMARK 465 GLU A 5 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 ASN A 67 13.04 55.79 REMARK 500 ALA A 114 40.19 73.97 REMARK 500 LYS A 117 89.43 -58.57 REMARK 500 ASP A 217 70.20 57.90 REMARK 500 ARG A 235 63.80 -151.52 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 GLN A 260 ASP A 261 148.77 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 262 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 ND1 REMARK 620 2 HIS A 151 ND1 94.0 REMARK 620 3 ASP A 161 OD1 99.0 123.0 REMARK 620 4 HOH A 322 O 130.2 97.5 114.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: NULL REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: NULL REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 263 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BGX RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID FROM E. COLI REMARK 900 RELATED ID: 2BH7 RELATED DB: PDB REMARK 900 SEMET DERIVATIVE OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID FROM REMARK 900 E. COLI REMARK 900 RELATED ID: 3D2Y RELATED DB: PDB DBREF 3D2Z A 3 261 UNP P75820 AMID_ECOLI 18 276 DBREF 3D2Z B 1 3 PDB 3D2Z 3D2Z 1 3 SEQADV 3D2Z MET A 1 UNP P75820 EXPRESSION TAG SEQADV 3D2Z GLY A 2 UNP P75820 EXPRESSION TAG SEQRES 1 A 261 MET 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 MET THR PRO ARG SEQRES 18 A 261 GLU GLN ARG ARG VAL ILE MET ALA PHE GLN MET 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 SEQRES 1 B 3 ALA FGA LYS HET FGA B 2 9 HET ZN A 262 1 HET ZN A 263 1 HET CL A 264 1 HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETSYN FGA D-GLUTAMIC ACID FORMUL 2 FGA C5 H9 N O4 FORMUL 3 ZN 2(ZN 2+) FORMUL 5 CL CL 1- FORMUL 6 HOH *76(H2 O) HELIX 1 1 ASP A 40 THR A 49 1 10 HELIX 2 2 GLU A 123 HIS A 142 1 20 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 A 2 ILE A 8 LYS A 11 0 SHEET 2 A 2 TYR A 14 ASP A 17 -1 O LEU A 16 N VAL A 9 SHEET 1 B 5 TRP A 73 GLN A 74 0 SHEET 2 B 5 TYR A 57 VAL A 59 -1 N LEU A 58 O TRP A 73 SHEET 3 B 5 SER A 100 LEU A 105 1 O GLU A 104 N TYR A 57 SHEET 4 B 5 VAL A 31 TYR A 36 1 N VAL A 33 O ILE A 101 SHEET 5 B 5 VAL A 148 ALA A 150 1 O VAL A 149 N LEU A 32 SHEET 1 C 2 ARG A 65 TYR A 66 0 SHEET 2 C 2 LYS A 69 PRO A 70 -1 O LYS A 69 N TYR A 66 SHEET 1 D 2 ALA A 89 TRP A 90 0 SHEET 2 D 2 ALA A 93 THR A 94 -1 O ALA A 93 N TRP A 90 SHEET 1 E 2 TRP A 110 LYS A 112 0 SHEET 2 E 2 LYS A 117 PHE A 119 -1 O TYR A 118 N GLN A 111 LINK C ALA B 1 N FGA B 2 1555 1555 1.34 LINK CD FGA B 2 N LYS B 3 1555 1555 1.33 LINK ND1 HIS A 35 ZN ZN A 262 1555 1555 2.25 LINK ND1 HIS A 151 ZN ZN A 262 1555 1555 1.95 LINK OD1 ASP A 161 ZN ZN A 262 1555 1555 1.93 LINK ZN ZN A 262 O HOH A 322 1555 1555 2.00 CISPEP 1 ASP A 161 PRO A 162 0 4.07 SITE 1 AC1 3 HIS A 35 HIS A 151 ASP A 161 SITE 1 AC2 2 ASP A 17 ARG A 20 SITE 1 AC3 4 HIS A 35 HIS A 151 ASP A 161 HOH A 322 SITE 1 AC4 3 ASP A 17 ARG A 20 HOH A 337 CRYST1 89.160 89.160 183.640 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 0.011216 0.006475 0.000000 0.00000 SCALE2 0.000000 0.012951 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005445 0.00000