HEADER HYDROLASE 28-MAR-12 4AOK TITLE CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA-DECARBOXYLASE ACTIVE SITE TITLE 2 REVEALED BY PROTEIN-LIGAND COMPLEXES: 1-METHYL-L-ASPARTATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTATE 1-DECARBOXYLASE BETA CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 SYNONYM: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN; COMPND 5 EC: 4.1.1.11; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN; COMPND 9 CHAIN: B, E; COMPND 10 SYNONYM: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN; COMPND 11 EC: 4.1.1.11; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: POSTTRANSLATIONAL MAIN CHAIN BREAK BETWEEN CHAIN A COMPND 14 GLY24 AND CHAIN B SER25. SAME FOR CHAINS D AND E. SERINE 25 MODIFIED COMPND 15 TO YIELD A PYRUVOYL COFACTOR IN BOTH CASES. IN THIS STRUCTURE THE COMPND 16 BOUND LIGAND HAS FORMED A COVALENT IMINIUM INTERMEDIATE WITH PYR 25 COMPND 17 IN BOTH SUBUNITS IN THE ASYMMETRIC UNIT. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 14 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS HYDROLASE, ASPARTATE DECARBOXYLASE, AMINO ACID METABOLISM, PROTEIN- KEYWDS 2 DERIVED COFACTOR. EXPDTA X-RAY DIFFRACTION AUTHOR B.A.YORKE,D.C.F.MONTEIRO,A.R.PEARSON,M.E.WEBB REVDAT 3 23-OCT-24 4AOK 1 REMARK REVDAT 2 20-DEC-23 4AOK 1 LINK REVDAT 1 31-OCT-12 4AOK 0 JRNL AUTH B.A.YORKE,D.C.F.MONTEIRO,A.R.PEARSON,M.E.WEBB JRNL TITL CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA DECARBOXYLASE JRNL TITL 2 ACTIVE SITE REVEALED BY PROTEIN-LIGAND COMPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 49762 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2665 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3234 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1874 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -0.62000 REMARK 3 B12 (A**2) : 0.21000 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): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.265 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1986 ; 0.025 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1310 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2698 ; 2.143 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3184 ; 1.159 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 6.744 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;29.718 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;12.481 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.024 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 302 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2270 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3294 ; 7.408 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 58 ;34.690 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3377 ;12.855 ; 5.000 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 4AOK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1290051859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97779 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52548 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 53.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 1.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1AW8 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MG/ML ASPARTATE-ALPHA-DECARBOXYLASE REMARK 280 IN 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 3.8, PH 4.2 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 71.96667 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 143.93333 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 107.95000 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 179.91667 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 35.98333 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 71.96667 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 143.93333 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 179.91667 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 107.95000 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 35.98333 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -134.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E 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 -35.65000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 61.74761 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 35.98333 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 -16 REMARK 465 ARG A -15 REMARK 465 GLY A -14 REMARK 465 SER A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 VAL A -4 REMARK 465 PRO A -3 REMARK 465 GLN B 124 REMARK 465 VAL B 125 REMARK 465 ALA B 126 REMARK 465 MET D -16 REMARK 465 ARG D -15 REMARK 465 GLY D -14 REMARK 465 SER D -13 REMARK 465 HIS D -12 REMARK 465 HIS D -11 REMARK 465 HIS D -10 REMARK 465 HIS D -9 REMARK 465 HIS D -8 REMARK 465 HIS D -7 REMARK 465 GLY D -6 REMARK 465 LEU D -5 REMARK 465 VAL D -4 REMARK 465 PRO D -3 REMARK 465 ARG D -2 REMARK 465 GLY D -1 REMARK 465 THR E 117 REMARK 465 ALA E 118 REMARK 465 LYS E 119 REMARK 465 ALA E 120 REMARK 465 ILE E 121 REMARK 465 PRO E 122 REMARK 465 VAL E 123 REMARK 465 GLN E 124 REMARK 465 VAL E 125 REMARK 465 ALA E 126 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A -2 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 23 CB CG CD OE1 OE2 REMARK 470 LYS B 119 CG CD CE NZ REMARK 470 ARG E 116 CG CD NE CZ NH1 NH2 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 B 2004 O HOH B 2033 1.82 REMARK 500 O HOH B 2002 O HOH B 2056 1.98 REMARK 500 O GLY A -1 OE1 GLU E 97 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 OD2 ASP E 111 OD2 ASP E 111 7555 2.10 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 HIS A 21 CG HIS A 21 CD2 0.060 REMARK 500 GLU B 40 CD GLU B 40 OE2 0.087 REMARK 500 SER D 0 C SER D 0 O 0.162 REMARK 500 HIS D 21 CG HIS D 21 CD2 0.066 REMARK 500 GLU E 40 CD GLU E 40 OE1 0.075 REMARK 500 GLU E 40 CD GLU E 40 OE2 0.080 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 3A5 B 25 O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 PHE B 32 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG B 67 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 99 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 102 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 102 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG E 102 NE - CZ - NH1 ANGL. DEV. = -4.8 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 ARG A 12 39.62 71.53 REMARK 500 THR B 57 -149.85 -146.34 REMARK 500 ASP E 29 123.34 -38.52 REMARK 500 ASN E 41 3.61 80.84 REMARK 500 THR E 57 -152.31 -146.36 REMARK 500 LYS E 115 35.36 122.25 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 ALA B 120 ILE B 121 -149.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 (2Z,4S)-3-AZA-5-CARBOXYL-2-METHYL-4(METHYLCARBOXY)PENT-2-ENOYL REMARK 600 (3A5): RESIDUE 25 IN BOTH CHAINS B AND E HAS BEEN REMARK 600 POSTTRANSLATIONALLY MODIFIED TO A PYRUVOYL GROUP. THIS HAS REMARK 600 THEN SUBSEQUENTLY FORMED A COVALENT IMINIUM INTERMEDIATE REMARK 600 WITH THE LIGAND, 1-METHYL-L-ASPARTATE TO YIELD THE REMARK 600 MODIFIED AMINO ACID RESIDUE DESCRIBED HERE. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AW8 RELATED DB: PDB REMARK 900 PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE REMARK 900 RELATED ID: 1PPY RELATED DB: PDB REMARK 900 NATIVE PRECURSOR OF PYRUVOYL DEPENDENT ASPARTATEDECARBOXYLASE REMARK 900 RELATED ID: 1PQE RELATED DB: PDB REMARK 900 S25A MUTANT OF PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE REMARK 900 RELATED ID: 1PQF RELATED DB: PDB REMARK 900 GLYCINE 24 TO SERINE MUTATION OF ASPARTATE DECARBOXYLASE REMARK 900 RELATED ID: 1PQH RELATED DB: PDB REMARK 900 SERINE 25 TO THREONINE MUTATION OF ASPARTATE DECARBOXYLASE REMARK 900 RELATED ID: 1PT0 RELATED DB: PDB REMARK 900 UNPROCESSED PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE WITHAN REMARK 900 ALANINE INSERTION AT POSITION 26 REMARK 900 RELATED ID: 1PT1 RELATED DB: PDB REMARK 900 UNPROCESSED PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE REMARK 900 WITHHISTIDINE 11 MUTATED TO ALANINE REMARK 900 RELATED ID: 1PYQ RELATED DB: PDB REMARK 900 UNPROCESSED ASPARTATE DECARBOXYLASE MUTANT REMARK 900 RELATED ID: 1PYU RELATED DB: PDB REMARK 900 PROCESSED ASPARTATE DECARBOXYLASE MUTANT REMARK 900 RELATED ID: 4AON RELATED DB: PDB REMARK 900 CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA-DECARBOXYLASE ACTIVE REMARK 900 SITE REVEALED BY PROTEIN-LIGAND COMPLEXES: 1- METHYL-L-ASPARTATE REMARK 900 COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 HIS TAG PRESENT. DBREF 4AOK A 1 24 UNP P0A790 PAND_ECOKI 1 24 DBREF 4AOK B 25 126 UNP P0A790 PAND_ECOKI 25 126 DBREF 4AOK D 1 24 UNP P0A790 PAND_ECOKI 1 24 DBREF 4AOK E 25 126 UNP P0A790 PAND_ECOKI 25 126 SEQADV 4AOK MET A -16 UNP P0A790 EXPRESSION TAG SEQADV 4AOK ARG A -15 UNP P0A790 EXPRESSION TAG SEQADV 4AOK GLY A -14 UNP P0A790 EXPRESSION TAG SEQADV 4AOK SER A -13 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS A -12 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS A -11 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS A -10 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS A -9 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS A -8 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS A -7 UNP P0A790 EXPRESSION TAG SEQADV 4AOK GLY A -6 UNP P0A790 EXPRESSION TAG SEQADV 4AOK LEU A -5 UNP P0A790 EXPRESSION TAG SEQADV 4AOK VAL A -4 UNP P0A790 EXPRESSION TAG SEQADV 4AOK PRO A -3 UNP P0A790 EXPRESSION TAG SEQADV 4AOK ARG A -2 UNP P0A790 EXPRESSION TAG SEQADV 4AOK GLY A -1 UNP P0A790 EXPRESSION TAG SEQADV 4AOK SER A 0 UNP P0A790 EXPRESSION TAG SEQADV 4AOK MET D -16 UNP P0A790 EXPRESSION TAG SEQADV 4AOK ARG D -15 UNP P0A790 EXPRESSION TAG SEQADV 4AOK GLY D -14 UNP P0A790 EXPRESSION TAG SEQADV 4AOK SER D -13 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS D -12 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS D -11 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS D -10 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS D -9 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS D -8 UNP P0A790 EXPRESSION TAG SEQADV 4AOK HIS D -7 UNP P0A790 EXPRESSION TAG SEQADV 4AOK GLY D -6 UNP P0A790 EXPRESSION TAG SEQADV 4AOK LEU D -5 UNP P0A790 EXPRESSION TAG SEQADV 4AOK VAL D -4 UNP P0A790 EXPRESSION TAG SEQADV 4AOK PRO D -3 UNP P0A790 EXPRESSION TAG SEQADV 4AOK ARG D -2 UNP P0A790 EXPRESSION TAG SEQADV 4AOK GLY D -1 UNP P0A790 EXPRESSION TAG SEQADV 4AOK SER D 0 UNP P0A790 EXPRESSION TAG SEQRES 1 A 41 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY LEU VAL SEQRES 2 A 41 PRO ARG GLY SER MET ILE ARG THR MET LEU GLN GLY LYS SEQRES 3 A 41 LEU HIS ARG VAL LYS VAL THR HIS ALA ASP LEU HIS TYR SEQRES 4 A 41 GLU GLY SEQRES 1 B 102 3A5 CYS ALA ILE ASP GLN ASP PHE LEU ASP ALA ALA GLY SEQRES 2 B 102 ILE LEU GLU ASN GLU ALA ILE ASP ILE TRP ASN VAL THR SEQRES 3 B 102 ASN GLY LYS ARG PHE SER THR TYR ALA ILE ALA ALA GLU SEQRES 4 B 102 ARG GLY SER ARG ILE ILE SER VAL ASN GLY ALA ALA ALA SEQRES 5 B 102 HIS CYS ALA SER VAL GLY ASP ILE VAL ILE ILE ALA SER SEQRES 6 B 102 PHE VAL THR MET PRO ASP GLU GLU ALA ARG THR TRP ARG SEQRES 7 B 102 PRO ASN VAL ALA TYR PHE GLU GLY ASP ASN GLU MET LYS SEQRES 8 B 102 ARG THR ALA LYS ALA ILE PRO VAL GLN VAL ALA SEQRES 1 D 41 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY LEU VAL SEQRES 2 D 41 PRO ARG GLY SER MET ILE ARG THR MET LEU GLN GLY LYS SEQRES 3 D 41 LEU HIS ARG VAL LYS VAL THR HIS ALA ASP LEU HIS TYR SEQRES 4 D 41 GLU GLY SEQRES 1 E 102 3A5 CYS ALA ILE ASP GLN ASP PHE LEU ASP ALA ALA GLY SEQRES 2 E 102 ILE LEU GLU ASN GLU ALA ILE ASP ILE TRP ASN VAL THR SEQRES 3 E 102 ASN GLY LYS ARG PHE SER THR TYR ALA ILE ALA ALA GLU SEQRES 4 E 102 ARG GLY SER ARG ILE ILE SER VAL ASN GLY ALA ALA ALA SEQRES 5 E 102 HIS CYS ALA SER VAL GLY ASP ILE VAL ILE ILE ALA SER SEQRES 6 E 102 PHE VAL THR MET PRO ASP GLU GLU ALA ARG THR TRP ARG SEQRES 7 E 102 PRO ASN VAL ALA TYR PHE GLU GLY ASP ASN GLU MET LYS SEQRES 8 E 102 ARG THR ALA LYS ALA ILE PRO VAL GLN VAL ALA HET 3A5 B 25 18 HET 3A5 E 25 18 HETNAM 3A5 (2Z,4S)-3-AZA-5-CARBOXYL-2-METHYL-4(METHYLCARBOXY)PENT- HETNAM 2 3A5 2-ENOYL FORMUL 2 3A5 2(C8 H11 N O6) FORMUL 5 HOH *178(H2 O) HELIX 1 1 GLN B 30 GLY B 37 1 8 HELIX 2 2 ALA B 74 CYS B 78 5 5 HELIX 3 3 ASP B 95 TRP B 101 1 7 HELIX 4 4 THR B 117 ILE B 121 5 5 HELIX 5 5 GLN E 30 GLY E 37 1 8 HELIX 6 6 ALA E 74 CYS E 78 5 5 HELIX 7 7 ASP E 95 ARG E 99 1 5 SHEET 1 BA 6 ARG B 54 TYR B 58 0 SHEET 2 BA 6 ALA B 43 ASN B 48 -1 O ILE B 44 N THR B 57 SHEET 3 BA 6 ILE B 84 PRO B 94 -1 O ILE B 86 N TRP B 47 SHEET 4 BA 6 ILE A 2 LYS A 14 -1 O ARG A 3 N MET B 93 SHEET 5 BA 6 ASN B 104 GLU B 109 1 O ASN B 104 N LYS A 9 SHEET 6 BA 6 GLU B 113 LYS B 115 1 O GLU B 113 N GLU B 109 SHEET 1 BB 7 ARG B 54 TYR B 58 0 SHEET 2 BB 7 ALA B 43 ASN B 48 -1 O ILE B 44 N THR B 57 SHEET 3 BB 7 ILE B 84 PRO B 94 -1 O ILE B 86 N TRP B 47 SHEET 4 BB 7 ILE A 2 LYS A 14 -1 O ARG A 3 N MET B 93 SHEET 5 BB 7 ILE E 84 PRO E 94 -1 O PHE E 90 N THR A 4 SHEET 6 BB 7 ALA E 43 ASN E 48 1 O ASP E 45 N ALA E 88 SHEET 7 BB 7 ARG E 54 TYR E 58 -1 O PHE E 55 N ILE E 46 SHEET 1 BC 8 ARG B 54 TYR B 58 0 SHEET 2 BC 8 ALA B 43 ASN B 48 -1 O ILE B 44 N THR B 57 SHEET 3 BC 8 ILE B 84 PRO B 94 -1 O ILE B 86 N TRP B 47 SHEET 4 BC 8 ILE A 2 LYS A 14 -1 O ARG A 3 N MET B 93 SHEET 5 BC 8 ILE E 84 PRO E 94 -1 O PHE E 90 N THR A 4 SHEET 6 BC 8 ILE D 2 LYS D 14 -1 O ARG D 3 N MET E 93 SHEET 7 BC 8 ASN E 104 GLU E 109 1 O ASN E 104 N LYS D 9 SHEET 8 BC 8 GLU E 113 MET E 114 -1 O GLU E 113 N GLU E 109 SHEET 1 AA 4 HIS A 17 ASP A 19 0 SHEET 2 AA 4 ILE B 69 ASN B 72 1 O VAL B 71 N ASP A 19 SHEET 3 AA 4 ALA B 27 ASP B 29 -1 O ALA B 27 N SER B 70 SHEET 4 AA 4 ILE B 60 ALA B 62 1 O ILE B 60 N ILE B 28 SHEET 1 DA 4 HIS D 17 ASP D 19 0 SHEET 2 DA 4 ILE E 69 ASN E 72 1 O VAL E 71 N ASP D 19 SHEET 3 DA 4 ALA E 27 ASP E 29 -1 O ALA E 27 N SER E 70 SHEET 4 DA 4 ILE E 60 ALA E 62 1 O ILE E 60 N ILE E 28 LINK C 3A5 B 25 N CYS B 26 1555 1555 1.43 LINK C 3A5 E 25 N CYS E 26 1555 1555 1.34 CRYST1 71.300 71.300 215.900 90.00 90.00 120.00 P 61 2 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 0.014025 0.008097 0.000000 0.00000 SCALE2 0.000000 0.016195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004632 0.00000