PDB Short entry for 1LKC HEADER LYASE 24-APR-02 1LKC TITLE CRYSTAL STRUCTURE OF L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE FROM TITLE 2 SALMONELLA ENTERICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COBD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA; SOURCE 3 ORGANISM_TAXID: 28901; SOURCE 4 GENE: COBD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COBD, L-THREONINE-O-3-PHOSPHATE, 1-AMINO-2-PROPANOL-PHOSPHATE, PLP, KEYWDS 2 DECARBOXYLASE, COBALAMIN, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.G.CHEONG,C.B.BAUER,K.R.BRUSHABER,J.C.ESCALANTE-SEMERENA,I.RAYMENT REVDAT 5 16-NOV-11 1LKC 1 HETATM REVDAT 4 13-JUL-11 1LKC 1 VERSN REVDAT 3 24-FEB-09 1LKC 1 VERSN REVDAT 2 01-APR-03 1LKC 1 JRNL REVDAT 1 01-MAY-02 1LKC 0 SPRSDE 01-MAY-02 1LKC 1KUS JRNL AUTH C.G.CHEONG,C.B.BAUER,K.R.BRUSHABER,J.C.ESCALANTE-SEMERENA, JRNL AUTH 2 I.RAYMENT JRNL TITL THREE-DIMENSIONAL STRUCTURE OF THE L-THREONINE-O-3-PHOSPHATE JRNL TITL 2 DECARBOXYLASE (COBD) ENZYME FROM SALMONELLA ENTERICA. JRNL REF BIOCHEMISTRY V. 41 4798 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11939774 JRNL DOI 10.1021/BI012111W REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 37844 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1899 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.59700 REMARK 3 B22 (A**2) : 0.12800 REMARK 3 B33 (A**2) : 8.46900 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.68 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.036 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.611 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.779 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.210 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 56.08 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : PI.PARA REMARK 3 PARAMETER FILE 4 : PLPLYS.PARA REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : PI.TOPO REMARK 3 TOPOLOGY FILE 4 : PLPLYS.TOPO REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LKC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-02. REMARK 100 THE RCSB ID CODE IS RCSB016025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94645, 0.97915, 0.97926, 1.0205 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37844 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM PHOSPHATE, KCL, GLYCEROL, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+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 1.000000 0.000000 0.000000 33.98000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.77500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.61500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.98000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.77500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.61500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.98000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.77500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.61500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.98000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.77500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.61500 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 -1.000000 0.000000 0.000000 67.96000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 117.23000 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 A1324 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 ALA A 2 REMARK 465 LEU A 3 REMARK 465 PHE A 4 REMARK 465 ASN A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 363 REMARK 465 ASP A 364 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 ASN A 11 CG OD1 ND2 REMARK 470 ARG A 13 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 PRO A 15 CG CD REMARK 470 LEU A 36 CG CD1 CD2 REMARK 470 ARG A 44 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 GLU A 141 CG CD OE1 OE2 REMARK 470 ASN A 179 CG OD1 ND2 REMARK 470 LYS A 203 CG CD CE NZ REMARK 470 ASP A 204 CG OD1 OD2 REMARK 470 GLN A 242 CG CD OE1 NE2 REMARK 470 GLN A 243 CG CD OE1 NE2 REMARK 470 SER A 263 OG REMARK 470 ARG A 279 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 286 CG CD OE1 NE2 REMARK 470 GLU A 307 CG CD OE1 OE2 REMARK 470 ARG A 313 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 OD1 ASP A 190 O2 EDO A 701 2.14 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 238 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 238 NE - CZ - NH2 ANGL. DEV. = -3.8 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 ASN A 32 72.03 -116.32 REMARK 500 ARG A 224 91.75 67.19 REMARK 500 GLU A 275 -79.90 -85.71 REMARK 500 ALA A 297 -149.74 -118.74 REMARK 500 ASN A 298 41.59 -89.43 REMARK 500 SER A 333 -9.95 -55.94 REMARK 500 ARG A 341 -141.33 -122.20 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 TYR A 111 0.06 SIDE CHAIN 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 PO4 A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KUS RELATED DB: PDB REMARK 900 THIS IS MORE REFINED STRUCTURE OF 1KUS REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHORS, THE GENBANK ENTRY IS IN REMARK 999 ERROR BECAUSE THE ORIGINAL DNA SEQUENCE HAD REMARK 999 SOME ERRORS. THE ELECTRON DENSITY ALSO SUPPORTS REMARK 999 IT. THE NEW SEQUENCE IS GLN25, SER30, VAL42, ARG44 REMARK 999 AND ALA45. ARG44 LACKS SIDE CHAIN DENSITY. REMARK 999 REMARK 999 THE ORGANISM NAME IN THIS GENBANK ENTRY IS REMARK 999 SALMONELLA TYPHIMURIUM. SALMONELLA TYPHIMURIUM REMARK 999 HAS BEEN CHANGED TO SALMONELLA ENTERICA. THEREFORE, REMARK 999 THE TWO NAMES ARE SAME. DBREF 1LKC A 1 364 UNP P97084 COBD_SALTY 1 364 SEQADV 1LKC GLN A 25 UNP P97084 HIS 25 SEE REMARK 999 SEQADV 1LKC SER A 30 UNP P97084 THR 30 SEE REMARK 999 SEQADV 1LKC VAL A 42 UNP P97084 LEU 42 SEE REMARK 999 SEQADV 1LKC ARG A 44 UNP P97084 PRO 44 SEE REMARK 999 SEQADV 1LKC ALA A 45 UNP P97084 PRO 45 SEE REMARK 999 SEQRES 1 A 364 MET ALA LEU PHE ASN THR ALA HIS GLY GLY ASN ILE ARG SEQRES 2 A 364 GLU PRO ALA THR VAL LEU GLY ILE SER PRO ASP GLN LEU SEQRES 3 A 364 LEU ASP PHE SER ALA ASN ILE ASN PRO LEU GLY MET PRO SEQRES 4 A 364 VAL SER VAL LYS ARG ALA LEU ILE ASP ASN LEU ASP CYS SEQRES 5 A 364 ILE GLU ARG TYR PRO ASP ALA ASP TYR PHE HIS LEU HIS SEQRES 6 A 364 GLN ALA LEU ALA ARG HIS HIS GLN VAL PRO ALA SER TRP SEQRES 7 A 364 ILE LEU ALA GLY ASN GLY GLU THR GLU SER ILE PHE THR SEQRES 8 A 364 VAL ALA SER GLY LEU LYS PRO ARG ARG ALA MET ILE VAL SEQRES 9 A 364 THR PRO GLY PHE ALA GLU TYR GLY ARG ALA LEU ALA GLN SEQRES 10 A 364 SER GLY CYS GLU ILE ARG ARG TRP SER LEU ARG GLU ALA SEQRES 11 A 364 ASP GLY TRP GLN LEU THR ASP ALA ILE LEU GLU ALA LEU SEQRES 12 A 364 THR PRO ASP LEU ASP CYS LEU PHE LEU CYS THR PRO ASN SEQRES 13 A 364 ASN PRO THR GLY LEU LEU PRO GLU ARG PRO LEU LEU GLN SEQRES 14 A 364 ALA ILE ALA ASP ARG CYS LYS SER LEU ASN ILE ASN LEU SEQRES 15 A 364 ILE LEU ASP GLU ALA PHE ILE ASP PHE ILE PRO HIS GLU SEQRES 16 A 364 THR GLY PHE ILE PRO ALA LEU LYS ASP ASN PRO HIS ILE SEQRES 17 A 364 TRP VAL LEU ARG SER LEU THR LYS PHE TYR ALA ILE PRO SEQRES 18 A 364 GLY LEU ARG LEU GLY TYR LEU VAL ASN SER ASP ASP ALA SEQRES 19 A 364 ALA MET ALA ARG MET ARG ARG GLN GLN MET PRO TRP SER SEQRES 20 A 364 VAL ASN ALA LEU ALA ALA LEU ALA GLY GLU VAL ALA LEU SEQRES 21 A 364 GLN ASP SER ALA TRP GLN GLN ALA THR TRP HIS TRP LEU SEQRES 22 A 364 ARG GLU GLU GLY ALA ARG PHE TYR GLN ALA LEU CYS GLN SEQRES 23 A 364 LEU PRO LEU LEU THR VAL TYR PRO GLY ARG ALA ASN TYR SEQRES 24 A 364 LEU LEU LEU ARG CYS GLU ARG GLU ASP ILE ASP LEU GLN SEQRES 25 A 364 ARG ARG LEU LEU THR GLN ARG ILE LEU ILE ARG SER CYS SEQRES 26 A 364 ALA ASN TYR PRO GLY LEU ASP SER ARG TYR TYR ARG VAL SEQRES 27 A 364 ALA ILE ARG SER ALA ALA GLN ASN GLU ARG LEU LEU ALA SEQRES 28 A 364 ALA LEU ARG ASN VAL LEU THR GLY ILE ALA PRO ALA ASP HET PO4 A 700 5 HET PLP A 800 15 HET EDO A 701 4 HET EDO A 702 4 HETNAM PO4 PHOSPHATE ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PO4 O4 P 3- FORMUL 3 PLP C8 H10 N O6 P FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 HOH *215(H2 O) HELIX 1 1 ILE A 12 GLY A 20 1 9 HELIX 2 2 SER A 22 LEU A 26 5 5 HELIX 3 3 PRO A 39 ASN A 49 1 11 HELIX 4 4 LEU A 50 ARG A 55 5 6 HELIX 5 5 TYR A 61 GLN A 73 1 13 HELIX 6 6 PRO A 75 SER A 77 5 3 HELIX 7 7 GLY A 84 LYS A 97 1 14 HELIX 8 8 ALA A 109 SER A 118 1 10 HELIX 9 9 ARG A 128 GLY A 132 5 5 HELIX 10 10 ASP A 137 LEU A 143 1 7 HELIX 11 11 GLU A 164 LEU A 178 1 15 HELIX 12 12 PHE A 188 ILE A 192 5 5 HELIX 13 13 PHE A 198 LEU A 202 5 5 HELIX 14 14 ASP A 232 GLN A 243 1 12 HELIX 15 15 ASN A 249 LEU A 260 1 12 HELIX 16 16 ALA A 264 LEU A 287 1 24 HELIX 17 17 ASP A 310 GLN A 318 1 9 HELIX 18 18 SER A 342 THR A 358 1 17 SHEET 1 A 2 LEU A 27 ASP A 28 0 SHEET 2 A 2 ILE A 320 LEU A 321 1 O LEU A 321 N LEU A 27 SHEET 1 B 7 ILE A 79 GLY A 82 0 SHEET 2 B 7 GLY A 226 VAL A 229 -1 O GLY A 226 N GLY A 82 SHEET 3 B 7 ILE A 208 SER A 213 -1 N ARG A 212 O TYR A 227 SHEET 4 B 7 ASN A 181 ASP A 185 1 N LEU A 184 O TRP A 209 SHEET 5 B 7 CYS A 149 CYS A 153 1 N LEU A 152 O ASP A 185 SHEET 6 B 7 ARG A 100 THR A 105 1 N MET A 102 O CYS A 149 SHEET 7 B 7 GLU A 121 SER A 126 1 O ARG A 123 N ALA A 101 SHEET 1 C 4 LEU A 290 VAL A 292 0 SHEET 2 C 4 TYR A 299 CYS A 304 -1 O ARG A 303 N THR A 291 SHEET 3 C 4 TYR A 335 ALA A 339 -1 O TYR A 336 N LEU A 302 SHEET 4 C 4 ARG A 323 SER A 324 -1 N ARG A 323 O ARG A 337 LINK NZ LYS A 216 C4A PLP A 800 1555 1555 1.31 CISPEP 1 THR A 105 PRO A 106 0 -0.43 CISPEP 2 THR A 154 PRO A 155 0 -0.11 CISPEP 3 ASN A 157 PRO A 158 0 2.40 SITE 1 AC1 8 HIS A 8 GLY A 9 ASN A 157 ARG A 323 SITE 2 AC1 8 TYR A 328 ARG A 337 HOH A 858 HOH A 917 SITE 1 AC2 14 TYR A 56 GLY A 84 GLU A 85 THR A 86 SITE 2 AC2 14 PHE A 108 CYS A 153 ASN A 157 ASP A 185 SITE 3 AC2 14 ALA A 187 PHE A 188 SER A 213 THR A 215 SITE 4 AC2 14 LYS A 216 ARG A 224 SITE 1 AC3 6 ASP A 190 ARG A 212 SER A 213 TYR A 227 SITE 2 AC3 6 HOH A 820 HOH A 822 SITE 1 AC4 6 LEU A 152 CYS A 153 ASN A 156 PRO A 163 SITE 2 AC4 6 HOH A 809 HOH A1201 CRYST1 67.960 101.550 117.230 90.00 90.00 90.00 I 2 2 2 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 0.014715 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008530 0.00000