HEADER HYDROLASE 09-MAY-08 3D2Y TITLE COMPLEX OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID FROM E.COLI WITH TITLE 2 THE SUBSTRATE ANHYDRO-N-ACETYLMURAMIC ACID-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: ANHYDRO-N-ACETYLMURAMIC ACID-L-ALA-D-GAMMA-GLU-L-LYS; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; 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 3D2Y 1 REMARK SEQADV LINK REVDAT 4 27-JUL-11 3D2Y 1 HETNAM HETSYN REVDAT 3 13-JUL-11 3D2Y 1 VERSN REVDAT 2 16-MAR-10 3D2Y 1 JRNL REVDAT 1 16-JUN-09 3D2Y 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 40210 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2136 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2620 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2098 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 308 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : 0.38000 REMARK 3 B12 (A**2) : -0.13000 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): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.354 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2198 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3000 ; 1.494 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 266 ; 6.582 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;34.900 ;23.704 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 350 ;16.669 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.663 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 319 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1709 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1033 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1464 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 216 ; 0.186 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 83 ; 0.201 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.117 ; 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): 1366 ; 2.509 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2137 ; 3.197 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 962 ; 2.799 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 858 ; 3.924 ; 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 : 9 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 13 REMARK 3 ORIGIN FOR THE GROUP (A): 39.9540 13.9260 64.2990 REMARK 3 T TENSOR REMARK 3 T11: 0.1755 T22: 0.0834 REMARK 3 T33: 0.1582 T12: 0.2044 REMARK 3 T13: -0.0482 T23: -0.1959 REMARK 3 L TENSOR REMARK 3 L11: 23.0125 L22: 16.2316 REMARK 3 L33: 2.9413 L12: 3.7807 REMARK 3 L13: 0.4453 L23: -6.6930 REMARK 3 S TENSOR REMARK 3 S11: -1.0101 S12: -0.9069 S13: 0.3139 REMARK 3 S21: -0.0810 S22: 0.2557 S23: -1.0070 REMARK 3 S31: 0.6546 S32: -0.8856 S33: 0.7544 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 14 A 65 REMARK 3 ORIGIN FOR THE GROUP (A): 36.2140 35.8370 84.3690 REMARK 3 T TENSOR REMARK 3 T11: 0.0148 T22: 0.0750 REMARK 3 T33: 0.0027 T12: 0.0570 REMARK 3 T13: -0.0428 T23: -0.0420 REMARK 3 L TENSOR REMARK 3 L11: 0.4718 L22: 0.4859 REMARK 3 L33: 2.2103 L12: 0.4056 REMARK 3 L13: 0.7637 L23: 1.0221 REMARK 3 S TENSOR REMARK 3 S11: 0.0389 S12: 0.0549 S13: -0.0883 REMARK 3 S21: 0.0864 S22: 0.1163 S23: -0.2049 REMARK 3 S31: 0.0808 S32: 0.2517 S33: -0.1552 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 66 A 108 REMARK 3 ORIGIN FOR THE GROUP (A): 34.9010 39.3360 86.8430 REMARK 3 T TENSOR REMARK 3 T11: 0.0171 T22: 0.0511 REMARK 3 T33: -0.0031 T12: 0.0329 REMARK 3 T13: -0.0345 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 1.7369 L22: 0.1626 REMARK 3 L33: 1.3047 L12: -0.0563 REMARK 3 L13: 1.3895 L23: -0.2060 REMARK 3 S TENSOR REMARK 3 S11: 0.0320 S12: 0.0688 S13: -0.0306 REMARK 3 S21: 0.0054 S22: 0.0001 S23: -0.0126 REMARK 3 S31: 0.0624 S32: 0.1134 S33: -0.0320 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 109 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): 27.1440 57.2950 103.5990 REMARK 3 T TENSOR REMARK 3 T11: 0.1779 T22: 0.0839 REMARK 3 T33: 0.1544 T12: 0.2256 REMARK 3 T13: -0.0371 T23: -0.1922 REMARK 3 L TENSOR REMARK 3 L11: 37.1662 L22: 52.5621 REMARK 3 L33: 30.1303 L12: 0.9934 REMARK 3 L13: -23.6165 L23: 26.9155 REMARK 3 S TENSOR REMARK 3 S11: 1.0823 S12: -0.4001 S13: 2.2517 REMARK 3 S21: 1.5500 S22: -1.2273 S23: 1.6493 REMARK 3 S31: -0.6493 S32: -1.3831 S33: 0.1450 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 119 A 140 REMARK 3 ORIGIN FOR THE GROUP (A): 42.9940 48.3960 87.9820 REMARK 3 T TENSOR REMARK 3 T11: -0.0194 T22: 0.0609 REMARK 3 T33: 0.0052 T12: 0.0043 REMARK 3 T13: -0.0521 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.7437 L22: 1.1889 REMARK 3 L33: 3.1218 L12: -0.5612 REMARK 3 L13: -0.1801 L23: 1.2267 REMARK 3 S TENSOR REMARK 3 S11: -0.0799 S12: 0.0427 S13: -0.0180 REMARK 3 S21: -0.0423 S22: 0.0447 S23: -0.1620 REMARK 3 S31: -0.2426 S32: 0.1716 S33: 0.0352 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 141 A 198 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0410 57.9410 81.6780 REMARK 3 T TENSOR REMARK 3 T11: 0.0662 T22: 0.0182 REMARK 3 T33: 0.0336 T12: -0.0397 REMARK 3 T13: -0.0967 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.0927 L22: 0.4999 REMARK 3 L33: 1.4781 L12: -0.5976 REMARK 3 L13: 0.3589 L23: -0.1887 REMARK 3 S TENSOR REMARK 3 S11: -0.1914 S12: 0.0524 S13: 0.1983 REMARK 3 S21: 0.0693 S22: 0.0337 S23: -0.0969 REMARK 3 S31: -0.2761 S32: 0.1805 S33: 0.1577 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 199 A 235 REMARK 3 ORIGIN FOR THE GROUP (A): 19.1730 57.5900 83.2300 REMARK 3 T TENSOR REMARK 3 T11: 0.0693 T22: 0.0064 REMARK 3 T33: -0.0086 T12: 0.0594 REMARK 3 T13: -0.0585 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.9767 L22: 1.2552 REMARK 3 L33: 2.0199 L12: -0.1071 REMARK 3 L13: 0.3404 L23: -0.6159 REMARK 3 S TENSOR REMARK 3 S11: -0.1700 S12: -0.0784 S13: 0.0798 REMARK 3 S21: 0.0822 S22: 0.1115 S23: 0.1086 REMARK 3 S31: -0.2191 S32: -0.1381 S33: 0.0585 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 236 A 261 REMARK 3 ORIGIN FOR THE GROUP (A): 26.8990 62.5700 79.5820 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: -0.0508 REMARK 3 T33: 0.0306 T12: 0.0051 REMARK 3 T13: -0.1235 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 1.7769 L22: 1.5745 REMARK 3 L33: 2.7197 L12: -1.0616 REMARK 3 L13: -0.1665 L23: 0.1814 REMARK 3 S TENSOR REMARK 3 S11: -0.1586 S12: 0.1608 S13: 0.3161 REMARK 3 S21: 0.0193 S22: -0.1185 S23: -0.1628 REMARK 3 S31: -0.5816 S32: -0.0449 S33: 0.2770 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 4 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3280 39.0560 92.6700 REMARK 3 T TENSOR REMARK 3 T11: 0.0664 T22: 0.0830 REMARK 3 T33: 0.0053 T12: 0.0260 REMARK 3 T13: -0.0125 T23: 0.0172 REMARK 3 L TENSOR REMARK 3 L11: 11.4448 L22: 4.9066 REMARK 3 L33: 16.2091 L12: 2.8592 REMARK 3 L13: 7.6523 L23: 5.7716 REMARK 3 S TENSOR REMARK 3 S11: 0.0507 S12: -0.5937 S13: 0.1170 REMARK 3 S21: 0.5198 S22: -0.1434 S23: 0.0738 REMARK 3 S31: 0.2098 S32: -0.3969 S33: 0.0927 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 3D2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 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) : 0.978850 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42426 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 47.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.82500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 63.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 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 60.61133 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 121.22267 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 90.91700 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 151.52833 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 30.30567 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 60.61133 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 121.22267 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 151.52833 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 90.91700 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 30.30567 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 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: 6370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 0.500000 -0.866025 0.000000 44.13700 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 76.44753 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 151.52833 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 329 LIES ON A SPECIAL POSITION. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 393 O HOH A 417 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 28 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES 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 LYS A 6 88.95 -67.86 REMARK 500 ARG A 235 62.02 -152.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 AH0 B 1 -12.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL 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: 3D2Z RELATED DB: PDB DBREF 3D2Y A 3 261 UNP P75820 AMID_ECOLI 18 276 DBREF 3D2Y B 1 4 PDB 3D2Y 3D2Y 1 4 SEQADV 3D2Y MET A 1 UNP P75820 EXPRESSION TAG SEQADV 3D2Y 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 4 AH0 ALA FGA LYS HET AH0 B 1 18 HET FGA B 3 9 HET GOL A 262 6 HET GOL A 263 6 HETNAM AH0 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT- HETNAM 2 AH0 3-YLOXY)-PROPIONIC ACID HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM GOL GLYCEROL HETSYN AH0 1,6-ANHYDRO-N-ACETYLMURAMIC ACID HETSYN FGA D-GLUTAMIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 AH0 C11 H17 N O7 FORMUL 2 FGA C5 H9 N O4 FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *308(H2 O) HELIX 1 1 ASP A 40 THR A 49 1 10 HELIX 2 2 LEU A 96 ASP A 98 5 3 HELIX 3 3 GLU A 123 HIS A 142 1 20 HELIX 4 4 LYS A 144 GLU A 146 5 3 HELIX 5 5 HIS A 151 ALA A 155 1 5 HELIX 6 6 PRO A 167 GLN A 174 1 8 HELIX 7 7 ASP A 181 ALA A 190 1 10 HELIX 8 8 ASP A 199 GLY A 211 1 13 HELIX 9 9 THR A 219 ARG A 235 1 17 HELIX 10 10 ASP A 244 GLY A 259 1 16 SHEET 1 A 2 ILE A 8 GLU A 10 0 SHEET 2 A 2 GLN A 15 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 VAL A 59 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 ILE A 34 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 SER A 113 0 SHEET 2 E 2 VAL A 116 PHE A 119 -1 O VAL A 116 N SER A 113 LINK C AH0 B 1 N ALA B 2 1555 1555 1.34 LINK C ALA B 2 N FGA B 3 1555 1555 1.33 LINK CD FGA B 3 N LYS B 4 1555 1555 1.34 CISPEP 1 ASP A 161 PRO A 162 0 1.43 SITE 1 AC1 8 THR A 18 ARG A 20 GLN A 21 GLN A 74 SITE 2 AC1 8 LEU A 75 VAL A 76 PRO A 77 HOH A 499 SITE 1 AC2 6 GLN A 169 ALA A 172 GLN A 173 TRP A 179 SITE 2 AC2 6 ASP A 181 LYS A 257 CRYST1 88.274 88.274 181.834 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 0.011328 0.006540 0.000000 0.00000 SCALE2 0.000000 0.013081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005500 0.00000