HEADER TRANSFERASE 16-MAY-07 2Z1Y TITLE CRYSTAL STRUCTURE OF LYSN, ALPHA-AMINOADIPATE AMINOTRANSFERASE TITLE 2 (COMPLEXED WITH N-(5'-PHOSPHOPYRIDOXYL)-L-LEUCINE), FROM THERMUS TITLE 3 THERMOPHILUS HB27 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-AMINOADIPATE TRANSAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2-AMINOADIPATE AMINOTRANSFERASE,ALPHA-AMINOADIPATE COMPND 5 AMINOTRANSFERASE,AAA-AT,AADAT; COMPND 6 EC: 2.6.1.39; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB27; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 GENE: LYSN, TT_C0043; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 CODON-PLUS(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-LYSN7 KEYWDS ALPHA-AMINOADIPATE AMINOTRANSFERASE, THERMUS THERMOPHILUS, SUBSTRATE KEYWDS 2 SPECIFITY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.TOMITA,T.MIYAZAKI,T.MIYAGAWA,S.FUSHINOBU,T.KUZUYAMA,M.NISHIYAMA REVDAT 5 29-JAN-25 2Z1Y 1 COMPND SOURCE REMARK DBREF REVDAT 5 2 1 HET HETNAM HETSYN FORMUL REVDAT 5 3 1 HELIX SHEET LINK SITE REVDAT 5 4 1 ATOM REVDAT 4 01-NOV-23 2Z1Y 1 REVDAT 3 13-JUL-11 2Z1Y 1 REVDAT 2 24-FEB-09 2Z1Y 1 REVDAT 1 03-JUN-08 2Z1Y 0 JRNL AUTH T.TOMITA,T.MIYAZAKI,T.MIYAGAWA,S.FUSHINOBU,T.KUZUYAMA, JRNL AUTH 2 M.NISHIYAMA JRNL TITL MECHANISM OF BROAD SUBSTRATE SPECIFICITY OF JRNL TITL 2 ALPHA-AMINOADIPATE AMINOTRANSFERASE FROM THERMUS JRNL TITL 3 THERMOPHILUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.MIYAZAKI,J.MIYAZAKI,H.YAMANE,M.NISHIYAMA REMARK 1 TITL ALPHA-AMINOADIPATE AMINOTRANSFERASE FROM AN EXTREMELY REMARK 1 TITL 2 THERMOPHILIC BACTERIUM, THERMUS THERMOPHILUS REMARK 1 REF MICROBIOLOGY V. 150 2327 2004 REMARK 1 REFN ISSN 0026-2617 REMARK 1 PMID 15256574 REMARK 1 DOI 10.1099/MIC.0.27037-0 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 36.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 77545 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4188 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) : 5674 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 298 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6127 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 754 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.226 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 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): 6327 ; 0.015 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6225 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8557 ; 2.181 ; 1.875 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14297 ; 0.723 ; 1.743 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 789 ; 6.221 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ; 7.839 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1077 ;13.322 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 930 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7542 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1476 ; 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): 3162 ; 1.737 ; 1.466 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3162 ; 1.737 ; 1.466 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3946 ; 2.302 ; 2.629 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3947 ; 2.302 ; 2.629 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3165 ; 3.701 ; 1.912 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3162 ; 3.701 ; 1.913 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4611 ; 5.574 ; 3.299 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7274 ; 6.657 ;16.550 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7080 ; 6.568 ;15.090 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 REMARK 4 REMARK 4 2Z1Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000027418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : 0.10900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000 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) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : 0.32300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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: 2DTV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 4000, 0.1M TRIS-HCL (PH 7.0), REMARK 280 0.2M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 68.55350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.11450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.55350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.11450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 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 THR A 29 REMARK 465 GLN A 30 REMARK 465 ARG A 31 REMARK 465 MET B 1 REMARK 465 LYS B 2 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 LYS A 2 CG CD CE NZ REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 LEU A 28 CG CD1 CD2 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 OE2 GLU B 62 O HOH B 501 2.08 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 90 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 214 N - CA - CB ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG A 223 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 MET A 304 CG - SD - CE ANGL. DEV. = -17.8 DEGREES REMARK 500 ARG A 385 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 16 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 80 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 160 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 164 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 245 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 289 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 294 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 MET B 304 CG - SD - CE ANGL. DEV. = -31.8 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 ALA A 38 -89.94 -89.99 REMARK 500 PHE A 172 62.34 64.99 REMARK 500 LEU A 208 36.40 -97.76 REMARK 500 LEU A 240 -64.44 -147.35 REMARK 500 SER A 241 118.34 -163.08 REMARK 500 ASP A 267 14.85 -156.83 REMARK 500 LEU A 268 -60.67 69.07 REMARK 500 ASN A 348 44.44 70.73 REMARK 500 ALA B 38 -93.56 -92.50 REMARK 500 PHE B 172 64.24 63.62 REMARK 500 LEU B 208 39.60 -95.19 REMARK 500 LEU B 240 -64.19 -138.43 REMARK 500 SER B 241 116.79 -165.42 REMARK 500 ASP B 267 11.46 -152.18 REMARK 500 LEU B 268 -66.80 71.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 160 0.12 SIDE CHAIN REMARK 500 ARG B 138 0.08 SIDE CHAIN REMARK 500 ARG B 223 0.09 SIDE CHAIN REMARK 500 ARG B 310 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DTV RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH LEUCINE AND PYRIDOXAL 5'-PHOSPHATE. REMARK 900 RELATED ID: 2EGY RELATED DB: PDB REMARK 900 SUBSTRATE FREE FORM OF THE SAME PROTEIN. DBREF 2Z1Y A 1 397 UNP Q72LL6 LYSN_THET2 1 397 DBREF 2Z1Y B 1 397 UNP Q72LL6 LYSN_THET2 1 397 SEQRES 1 A 397 MET LYS PRO LEU SER TRP SER GLU ALA PHE GLY LYS GLY SEQRES 2 A 397 ALA GLY ARG ILE GLN ALA SER THR ILE ARG GLU LEU LEU SEQRES 3 A 397 LYS LEU THR GLN ARG PRO GLY ILE LEU SER PHE ALA GLY SEQRES 4 A 397 GLY LEU PRO ALA PRO GLU LEU PHE PRO LYS GLU GLU ALA SEQRES 5 A 397 ALA GLU ALA ALA ALA ARG ILE LEU ARG GLU LYS GLY GLU SEQRES 6 A 397 VAL ALA LEU GLN TYR SER PRO THR GLU GLY TYR ALA PRO SEQRES 7 A 397 LEU ARG ALA PHE VAL ALA GLU TRP ILE GLY VAL ARG PRO SEQRES 8 A 397 GLU GLU VAL LEU ILE THR THR GLY SER GLN GLN ALA LEU SEQRES 9 A 397 ASP LEU VAL GLY LYS VAL PHE LEU ASP GLU GLY SER PRO SEQRES 10 A 397 VAL LEU LEU GLU ALA PRO SER TYR MET GLY ALA ILE GLN SEQRES 11 A 397 ALA PHE ARG LEU GLN GLY PRO ARG PHE LEU THR VAL PRO SEQRES 12 A 397 ALA GLY GLU GLU GLY PRO ASP LEU ASP ALA LEU GLU GLU SEQRES 13 A 397 VAL LEU LYS ARG GLU ARG PRO ARG PHE LEU TYR LEU ILE SEQRES 14 A 397 PRO SER PHE GLN ASN PRO THR GLY GLY LEU THR PRO LEU SEQRES 15 A 397 PRO ALA ARG LYS ARG LEU LEU GLN MET VAL MET GLU ARG SEQRES 16 A 397 GLY LEU VAL VAL VAL GLU ASP ASP ALA TYR ARG GLU LEU SEQRES 17 A 397 TYR PHE GLY GLU ALA ARG LEU PRO SER LEU PHE GLU LEU SEQRES 18 A 397 ALA ARG GLU ALA GLY TYR PRO GLY VAL ILE TYR LEU GLY SEQRES 19 A 397 SER PHE SER LYS VAL LEU SER PRO GLY LEU ARG VAL ALA SEQRES 20 A 397 PHE ALA VAL ALA HIS PRO GLU ALA LEU GLN LYS LEU VAL SEQRES 21 A 397 GLN ALA LYS GLN GLY ALA ASP LEU HIS THR PRO MET LEU SEQRES 22 A 397 ASN GLN MET LEU VAL HIS GLU LEU LEU LYS GLU GLY PHE SEQRES 23 A 397 SER GLU ARG LEU GLU ARG VAL ARG ARG VAL TYR ARG GLU SEQRES 24 A 397 LYS ALA GLN ALA MET LEU HIS ALA LEU ASP ARG GLU VAL SEQRES 25 A 397 PRO LYS GLU VAL ARG TYR THR ARG PRO LYS GLY GLY MET SEQRES 26 A 397 PHE VAL TRP MET GLU LEU PRO LYS GLY LEU SER ALA GLU SEQRES 27 A 397 GLY LEU PHE ARG ARG ALA LEU GLU GLU ASN VAL ALA PHE SEQRES 28 A 397 VAL PRO GLY GLY PRO PHE PHE ALA ASN GLY GLY GLY GLU SEQRES 29 A 397 ASN THR LEU ARG LEU SER TYR ALA THR LEU ASP ARG GLU SEQRES 30 A 397 GLY ILE ALA GLU GLY VAL ARG ARG LEU GLY ARG ALA LEU SEQRES 31 A 397 LYS GLY LEU LEU ALA LEU VAL SEQRES 1 B 397 MET LYS PRO LEU SER TRP SER GLU ALA PHE GLY LYS GLY SEQRES 2 B 397 ALA GLY ARG ILE GLN ALA SER THR ILE ARG GLU LEU LEU SEQRES 3 B 397 LYS LEU THR GLN ARG PRO GLY ILE LEU SER PHE ALA GLY SEQRES 4 B 397 GLY LEU PRO ALA PRO GLU LEU PHE PRO LYS GLU GLU ALA SEQRES 5 B 397 ALA GLU ALA ALA ALA ARG ILE LEU ARG GLU LYS GLY GLU SEQRES 6 B 397 VAL ALA LEU GLN TYR SER PRO THR GLU GLY TYR ALA PRO SEQRES 7 B 397 LEU ARG ALA PHE VAL ALA GLU TRP ILE GLY VAL ARG PRO SEQRES 8 B 397 GLU GLU VAL LEU ILE THR THR GLY SER GLN GLN ALA LEU SEQRES 9 B 397 ASP LEU VAL GLY LYS VAL PHE LEU ASP GLU GLY SER PRO SEQRES 10 B 397 VAL LEU LEU GLU ALA PRO SER TYR MET GLY ALA ILE GLN SEQRES 11 B 397 ALA PHE ARG LEU GLN GLY PRO ARG PHE LEU THR VAL PRO SEQRES 12 B 397 ALA GLY GLU GLU GLY PRO ASP LEU ASP ALA LEU GLU GLU SEQRES 13 B 397 VAL LEU LYS ARG GLU ARG PRO ARG PHE LEU TYR LEU ILE SEQRES 14 B 397 PRO SER PHE GLN ASN PRO THR GLY GLY LEU THR PRO LEU SEQRES 15 B 397 PRO ALA ARG LYS ARG LEU LEU GLN MET VAL MET GLU ARG SEQRES 16 B 397 GLY LEU VAL VAL VAL GLU ASP ASP ALA TYR ARG GLU LEU SEQRES 17 B 397 TYR PHE GLY GLU ALA ARG LEU PRO SER LEU PHE GLU LEU SEQRES 18 B 397 ALA ARG GLU ALA GLY TYR PRO GLY VAL ILE TYR LEU GLY SEQRES 19 B 397 SER PHE SER LYS VAL LEU SER PRO GLY LEU ARG VAL ALA SEQRES 20 B 397 PHE ALA VAL ALA HIS PRO GLU ALA LEU GLN LYS LEU VAL SEQRES 21 B 397 GLN ALA LYS GLN GLY ALA ASP LEU HIS THR PRO MET LEU SEQRES 22 B 397 ASN GLN MET LEU VAL HIS GLU LEU LEU LYS GLU GLY PHE SEQRES 23 B 397 SER GLU ARG LEU GLU ARG VAL ARG ARG VAL TYR ARG GLU SEQRES 24 B 397 LYS ALA GLN ALA MET LEU HIS ALA LEU ASP ARG GLU VAL SEQRES 25 B 397 PRO LYS GLU VAL ARG TYR THR ARG PRO LYS GLY GLY MET SEQRES 26 B 397 PHE VAL TRP MET GLU LEU PRO LYS GLY LEU SER ALA GLU SEQRES 27 B 397 GLY LEU PHE ARG ARG ALA LEU GLU GLU ASN VAL ALA PHE SEQRES 28 B 397 VAL PRO GLY GLY PRO PHE PHE ALA ASN GLY GLY GLY GLU SEQRES 29 B 397 ASN THR LEU ARG LEU SER TYR ALA THR LEU ASP ARG GLU SEQRES 30 B 397 GLY ILE ALA GLU GLY VAL ARG ARG LEU GLY ARG ALA LEU SEQRES 31 B 397 LYS GLY LEU LEU ALA LEU VAL HET LEU A 401 9 HET PLP A 402 15 HET LEU B 401 9 HET PLP B 402 15 HETNAM LEU LEUCINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 LEU 2(C6 H13 N O2) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 7 HOH *754(H2 O) HELIX 1 AA1 SER A 5 PHE A 10 1 6 HELIX 2 AA2 GLY A 11 ILE A 17 5 7 HELIX 3 AA3 SER A 20 LYS A 27 1 8 HELIX 4 AA4 ALA A 43 PHE A 47 5 5 HELIX 5 AA5 PRO A 48 LEU A 68 1 21 HELIX 6 AA6 TYR A 76 GLY A 88 1 13 HELIX 7 AA7 ARG A 90 GLU A 92 5 3 HELIX 8 AA8 THR A 98 LEU A 112 1 15 HELIX 9 AA9 TYR A 125 LEU A 134 1 10 HELIX 10 AB1 ASP A 150 GLU A 161 1 12 HELIX 11 AB2 PRO A 181 ARG A 195 1 15 HELIX 12 AB3 SER A 217 ALA A 225 1 9 HELIX 13 AB4 HIS A 252 LEU A 268 1 17 HELIX 14 AB5 PRO A 271 LYS A 283 1 13 HELIX 15 AB6 GLY A 285 VAL A 312 1 28 HELIX 16 AB7 SER A 336 GLU A 347 1 12 HELIX 17 AB8 GLY A 355 PHE A 358 5 4 HELIX 18 AB9 ASP A 375 LEU A 396 1 22 HELIX 19 AC1 SER B 5 PHE B 10 1 6 HELIX 20 AC2 GLY B 11 ILE B 17 5 7 HELIX 21 AC3 SER B 20 LYS B 27 1 8 HELIX 22 AC4 LEU B 28 ARG B 31 5 4 HELIX 23 AC5 ALA B 43 PHE B 47 5 5 HELIX 24 AC6 PRO B 48 LEU B 68 1 21 HELIX 25 AC7 TYR B 76 GLY B 88 1 13 HELIX 26 AC8 ARG B 90 GLU B 92 5 3 HELIX 27 AC9 GLY B 99 LEU B 112 1 14 HELIX 28 AD1 TYR B 125 LEU B 134 1 10 HELIX 29 AD2 ASP B 150 GLU B 161 1 12 HELIX 30 AD3 PRO B 181 GLY B 196 1 16 HELIX 31 AD4 SER B 217 ALA B 225 1 9 HELIX 32 AD5 HIS B 252 LEU B 268 1 17 HELIX 33 AD6 PRO B 271 LYS B 283 1 13 HELIX 34 AD7 GLY B 285 VAL B 312 1 28 HELIX 35 AD8 SER B 336 GLU B 347 1 12 HELIX 36 AD9 GLY B 355 PHE B 358 5 4 HELIX 37 AE1 ASP B 375 LEU B 396 1 22 SHEET 1 AA1 2 LEU A 35 SER A 36 0 SHEET 2 AA1 2 VAL A 349 ALA A 350 1 O ALA A 350 N LEU A 35 SHEET 1 AA2 8 VAL A 94 THR A 97 0 SHEET 2 AA2 8 ALA A 247 VAL A 250 -1 O ALA A 249 N LEU A 95 SHEET 3 AA2 8 VAL A 230 SER A 235 -1 N TYR A 232 O VAL A 250 SHEET 4 AA2 8 VAL A 199 ASP A 202 1 N VAL A 199 O ILE A 231 SHEET 5 AA2 8 LEU A 166 LEU A 168 1 N LEU A 168 O ASP A 202 SHEET 6 AA2 8 PRO A 117 ALA A 122 1 N LEU A 119 O TYR A 167 SHEET 7 AA2 8 ARG A 138 GLY A 145 1 O LEU A 140 N VAL A 118 SHEET 8 AA2 8 GLY A 148 PRO A 149 -1 O GLY A 148 N GLY A 145 SHEET 1 AA3 4 ARG A 317 TYR A 318 0 SHEET 2 AA3 4 PHE A 326 GLU A 330 -1 O GLU A 330 N ARG A 317 SHEET 3 AA3 4 THR A 366 SER A 370 -1 O LEU A 367 N MET A 329 SHEET 4 AA3 4 VAL A 352 PRO A 353 -1 N VAL A 352 O ARG A 368 SHEET 1 AA4 2 LEU B 35 SER B 36 0 SHEET 2 AA4 2 VAL B 349 ALA B 350 1 O ALA B 350 N LEU B 35 SHEET 1 AA5 5 VAL B 94 THR B 97 0 SHEET 2 AA5 5 ALA B 247 VAL B 250 -1 O ALA B 249 N LEU B 95 SHEET 3 AA5 5 VAL B 230 SER B 235 -1 N TYR B 232 O VAL B 250 SHEET 4 AA5 5 VAL B 199 ASP B 202 1 N VAL B 199 O ILE B 231 SHEET 5 AA5 5 LEU B 166 LEU B 168 1 N LEU B 168 O ASP B 202 SHEET 1 AA6 3 PRO B 117 ALA B 122 0 SHEET 2 AA6 3 ARG B 138 GLY B 145 1 O LEU B 140 N VAL B 118 SHEET 3 AA6 3 GLY B 148 PRO B 149 -1 O GLY B 148 N GLY B 145 SHEET 1 AA7 4 ARG B 317 TYR B 318 0 SHEET 2 AA7 4 PHE B 326 GLU B 330 -1 O GLU B 330 N ARG B 317 SHEET 3 AA7 4 THR B 366 SER B 370 -1 O LEU B 369 N VAL B 327 SHEET 4 AA7 4 VAL B 352 PRO B 353 -1 N VAL B 352 O ARG B 368 LINK N LEU A 401 C4A PLP A 402 1555 1555 1.47 LINK N LEU B 401 C4A PLP B 402 1555 1555 1.46 CISPEP 1 ALA A 122 PRO A 123 0 -0.63 CISPEP 2 ASN A 174 PRO A 175 0 11.27 CISPEP 3 ALA B 122 PRO B 123 0 1.02 CISPEP 4 ASN B 174 PRO B 175 0 12.49 CRYST1 137.107 62.229 107.439 90.00 116.34 90.00 C 1 2 1 8 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 0.007294 0.000000 0.003611 0.00000 SCALE2 0.000000 0.016070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010386 0.00000