HEADER HYDROLASE 29-MAY-13 4KZF TITLE THE MECHANISM OF THE AMIDASES: THE EFFECT OF THE MUTATION E142L IN THE TITLE 2 AMIDASE FROM GEOBACILLUS PALLIDUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALIPHATIC AMIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACYLAMIDE AMIDOHYDROLASE; COMPND 5 EC: 3.5.1.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SP.; SOURCE 3 ORGANISM_TAXID: 1409; SOURCE 4 STRAIN: RAPC8; SOURCE 5 GENE: AMIE, AMI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ACTIVE SITE, CHLORIDE ION, CYSTEINE 166 OXIDATION, AMIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.W.WEBER,B.T.SEWELL,S.W.KIMANI,A.VARSANI,D.A.COWAN,R.HUNTER REVDAT 3 08-NOV-23 4KZF 1 REMARK SEQADV REVDAT 2 12-FEB-14 4KZF 1 JRNL REVDAT 1 21-AUG-13 4KZF 0 JRNL AUTH B.W.WEBER,S.W.KIMANI,A.VARSANI,D.A.COWAN,R.HUNTER, JRNL AUTH 2 G.A.VENTER,J.C.GUMBART,B.T.SEWELL JRNL TITL THE MECHANISM OF THE AMIDASES: MUTATING THE GLUTAMATE JRNL TITL 2 ADJACENT TO THE CATALYTIC TRIAD INACTIVATES THE ENZYME DUE JRNL TITL 3 TO SUBSTRATE MISPOSITIONING. JRNL REF J.BIOL.CHEM. V. 288 28514 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23946488 JRNL DOI 10.1074/JBC.M113.503284 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 33155 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1690 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2134 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2640 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.712 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2722 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2548 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3688 ; 1.941 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5879 ; 0.959 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 7.105 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;32.255 ;24.516 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 461 ;12.042 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;19.556 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3106 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 623 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4KZF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000079987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : XSCALE, D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 92.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.580 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2PLQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M SODIUM CITRATE, 0.4M SODIUM REMARK 280 CHLORIDE, 0.1M SODIUM ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 14555 -Y+1/2,-X+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 16555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 17555 X+1/2,Z+1/2,-Y+1/2 REMARK 290 18555 -X+1/2,Z+1/2,Y+1/2 REMARK 290 19555 -X+1/2,-Z+1/2,-Y+1/2 REMARK 290 20555 X+1/2,-Z+1/2,Y+1/2 REMARK 290 21555 Z+1/2,Y+1/2,-X+1/2 REMARK 290 22555 Z+1/2,-Y+1/2,X+1/2 REMARK 290 23555 -Z+1/2,Y+1/2,X+1/2 REMARK 290 24555 -Z+1/2,-Y+1/2,-X+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 65.48950 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 65.48950 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 65.48950 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 65.48950 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 65.48950 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 65.48950 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 65.48950 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 65.48950 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 65.48950 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 65.48950 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 65.48950 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 65.48950 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 65.48950 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 65.48950 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 65.48950 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 65.48950 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 65.48950 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 65.48950 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 65.48950 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 65.48950 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 65.48950 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 65.48950 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 65.48950 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 65.48950 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 65.48950 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 65.48950 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 44440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -310.0 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 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 -65.48950 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 -65.48950 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 65.48950 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 -65.48950 REMARK 350 BIOMT2 5 0.000000 0.000000 1.000000 -65.48950 REMARK 350 BIOMT3 5 0.000000 1.000000 0.000000 65.48950 REMARK 350 BIOMT1 6 0.000000 0.000000 1.000000 -65.48950 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 -65.48950 REMARK 350 BIOMT3 6 1.000000 0.000000 0.000000 65.48950 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 506 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 538 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 562 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 581 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 593 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 605 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 615 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 617 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 658 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 GLU A 340 REMARK 465 GLY A 341 REMARK 465 LYS A 342 REMARK 465 THR A 343 REMARK 465 LYS A 344 REMARK 465 GLU A 345 REMARK 465 ILE A 346 REMARK 465 GLY A 347 REMARK 465 VAL A 348 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 630 O HOH A 653 2.01 REMARK 500 O HOH A 511 O HOH A 625 2.02 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 TYR A 192 C TYR A 192 O 0.120 REMARK 500 TYR A 284 CE1 TYR A 284 CZ 0.084 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 241 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 265 CB - CG - OD2 ANGL. DEV. = 5.5 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 HIS A 26 -24.92 -141.17 REMARK 500 CYS A 166 -106.52 41.18 REMARK 500 ALA A 196 39.10 -73.29 REMARK 500 VAL A 226 -58.76 -124.90 REMARK 500 GLN A 271 -70.39 -123.78 REMARK 500 THR A 323 -97.81 -124.84 REMARK 500 CYS A 332 76.39 -152.17 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 CL A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GYN RELATED DB: PDB REMARK 900 THE SAME MUTANT IN THE PRESENCE OF PROPIONAMIDE REMARK 900 RELATED ID: 4GYL RELATED DB: PDB REMARK 900 THE MICHAEL ADDUCT WITH ACRYLAMIDE OF THE SAME MUTANT REMARK 900 RELATED ID: 2PLQ RELATED DB: PDB REMARK 900 THE WILD-TYPE AMIDASE FROM WHICH THE MUTANT WAS MADE DBREF 4KZF A 1 348 UNP Q9L543 AMIE_BACSP 1 348 SEQADV 4KZF LEU A 142 UNP Q9L543 GLU 142 ENGINEERED MUTATION SEQRES 1 A 348 MET ARG HIS GLY ASP ILE SER SER SER HIS ASP THR VAL SEQRES 2 A 348 GLY ILE ALA VAL VAL ASN TYR LYS MET PRO ARG LEU HIS SEQRES 3 A 348 THR LYS ALA GLU VAL ILE GLU ASN ALA LYS LYS ILE ALA SEQRES 4 A 348 ASP MET VAL VAL GLY MET LYS GLN GLY LEU PRO GLY MET SEQRES 5 A 348 ASP LEU VAL VAL PHE PRO GLU TYR SER THR MET GLY ILE SEQRES 6 A 348 MET TYR ASP GLN ASP GLU MET PHE ALA THR ALA ALA SER SEQRES 7 A 348 ILE PRO GLY GLU GLU THR ALA ILE PHE ALA GLU ALA CYS SEQRES 8 A 348 LYS LYS ALA ASP THR TRP GLY VAL PHE SER LEU THR GLY SEQRES 9 A 348 GLU LYS HIS GLU ASP HIS PRO ASN LYS ALA PRO TYR ASN SEQRES 10 A 348 THR LEU VAL LEU ILE ASN ASN LYS GLY GLU ILE VAL GLN SEQRES 11 A 348 LYS TYR ARG LYS ILE ILE PRO TRP CYS PRO ILE LEU GLY SEQRES 12 A 348 TRP TYR PRO GLY ASP THR THR TYR VAL THR GLU GLY PRO SEQRES 13 A 348 LYS GLY LEU LYS ILE SER LEU ILE VAL CYS ASP ASP GLY SEQRES 14 A 348 ASN TYR PRO GLU ILE TRP ARG ASP CYS ALA MET LYS GLY SEQRES 15 A 348 ALA GLU LEU ILE VAL ARG CYS GLN GLY TYR MET TYR PRO SEQRES 16 A 348 ALA LYS GLU GLN GLN ILE MET MET ALA LYS ALA MET ALA SEQRES 17 A 348 TRP ALA ASN ASN THR TYR VAL ALA VAL ALA ASN ALA THR SEQRES 18 A 348 GLY PHE ASP GLY VAL TYR SER TYR PHE GLY HIS SER ALA SEQRES 19 A 348 ILE ILE GLY PHE ASP GLY ARG THR LEU GLY GLU CYS GLY SEQRES 20 A 348 THR GLU GLU ASN GLY ILE GLN TYR ALA GLU VAL SER ILE SEQRES 21 A 348 SER GLN ILE ARG ASP PHE ARG LYS ASN ALA GLN SER GLN SEQRES 22 A 348 ASN HIS LEU PHE LYS LEU LEU HIS ARG GLY TYR THR GLY SEQRES 23 A 348 LEU ILE ASN SER GLY GLU GLY ASP ARG GLY VAL ALA GLU SEQRES 24 A 348 CYS PRO PHE ASP PHE TYR ARG THR TRP VAL LEU ASP ALA SEQRES 25 A 348 GLU LYS ALA ARG GLU ASN VAL GLU LYS ILE THR ARG SER SEQRES 26 A 348 THR VAL GLY THR ALA GLU CYS PRO ILE GLN GLY ILE PRO SEQRES 27 A 348 ASN GLU GLY LYS THR LYS GLU ILE GLY VAL HET CL A 401 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *205(H2 O) HELIX 1 1 THR A 27 LEU A 49 1 23 HELIX 2 2 ASP A 68 ALA A 76 1 9 HELIX 3 3 GLY A 81 ASP A 95 1 15 HELIX 4 4 PRO A 156 GLY A 158 5 3 HELIX 5 5 ASP A 167 ASN A 170 5 4 HELIX 6 6 TYR A 171 LYS A 181 1 11 HELIX 7 7 ALA A 196 ASN A 211 1 16 HELIX 8 8 ILE A 260 ALA A 270 1 11 HELIX 9 9 ASN A 274 LEU A 280 1 7 HELIX 10 10 GLY A 283 SER A 290 1 8 HELIX 11 11 PHE A 302 ASP A 311 1 10 HELIX 12 12 ASP A 311 THR A 323 1 13 SHEET 1 A 6 ILE A 128 ARG A 133 0 SHEET 2 A 6 TYR A 116 ILE A 122 -1 N LEU A 121 O VAL A 129 SHEET 3 A 6 TRP A 97 GLU A 105 -1 N GLU A 105 O TYR A 116 SHEET 4 A 6 MET A 52 VAL A 56 1 N ASP A 53 O TRP A 97 SHEET 5 A 6 THR A 12 ASN A 19 1 N ALA A 16 O LEU A 54 SHEET 6 A 6 GLY A 252 SER A 259 -1 O ALA A 256 N ILE A 15 SHEET 1 B 6 THR A 153 GLU A 154 0 SHEET 2 B 6 LYS A 160 VAL A 165 -1 O ILE A 161 N THR A 153 SHEET 3 B 6 LEU A 185 GLN A 190 1 O VAL A 187 N SER A 162 SHEET 4 B 6 TYR A 214 ASN A 219 1 O ALA A 216 N ARG A 188 SHEET 5 B 6 ALA A 234 ILE A 236 -1 O ALA A 234 N VAL A 217 SHEET 6 B 6 THR A 242 GLU A 245 -1 O LEU A 243 N ILE A 235 SHEET 1 C 2 THR A 221 PHE A 223 0 SHEET 2 C 2 SER A 228 PHE A 230 -1 O TYR A 229 N GLY A 222 CISPEP 1 ILE A 79 PRO A 80 0 -1.41 CISPEP 2 THR A 103 GLY A 104 0 8.86 CISPEP 3 HIS A 110 PRO A 111 0 -6.40 CISPEP 4 CYS A 139 PRO A 140 0 7.31 CISPEP 5 TYR A 194 PRO A 195 0 19.48 SITE 1 AC1 5 TYR A 60 LYS A 134 TRP A 138 LEU A 142 SITE 2 AC1 5 TRP A 144 CRYST1 130.979 130.979 130.979 90.00 90.00 90.00 P 42 3 2 24 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 0.007635 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007635 0.00000