HEADER LYASE 12-APR-00 1ET0 TITLE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-AMINO-4-DEOXYCHORISMATE LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADC LYASE; COMPND 5 ENGINEERED: YES 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: 562 KEYWDS PSEUDO BETA BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAI,H.MIZUTANI,I.MIYAHARA,K.HIROTSU,S.TAKEDA,K.H.JHEE, AUTHOR 2 T.YOSHIMURA,N.ESAKI REVDAT 3 13-JUL-11 1ET0 1 VERSN REVDAT 2 24-FEB-09 1ET0 1 VERSN REVDAT 1 19-JUL-00 1ET0 0 JRNL AUTH T.NAKAI,H.MIZUTANI,I.MIYAHARA,K.HIROTSU,S.TAKEDA,K.H.JHEE, JRNL AUTH 2 T.YOSHIMURA,N.ESAKI JRNL TITL THREE-DIMENSIONAL STRUCTURE OF 4-AMINO-4-DEOXYCHORISMATE JRNL TITL 2 LYASE FROM ESCHERICHIA COLI. JRNL REF J.BIOCHEM.(TOKYO) V. 128 29 2000 JRNL REFN ISSN 0021-924X JRNL PMID 10876155 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.M.GREEN,W.K.MERKEL,B.P.NICHOLS REMARK 1 TITL CHARACTERIZATION AND SEQUENCE OF ESCHERICHIA COLI PABC, THE REMARK 1 TITL 2 GENE ENCODING AMINODEOXYCHORISMATE LYASE, A PYRIDOXAL REMARK 1 TITL 3 PHOSPHATE-CONTAINING ENZYME REMARK 1 REF J.BACTERIOL. V. 174 5317 1992 REMARK 1 REFN ISSN 0021-9193 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 11893 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) : 0.196 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1210 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL 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 : 1947 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.43 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ET0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-00. REMARK 100 THE RCSB ID CODE IS RCSB010868. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-99 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 6.5 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 7.140 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.13500 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: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, 2-PROPANOL, SODIUM CITRATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+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 20.25000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.96500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER CONSTRUCTED FROM CHAIN A REMARK 300 A SYMMETRY PARTNER GENERATED BY THE TWO-FOLD. 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 TYR A 126 REMARK 465 PRO A 127 REMARK 465 ALA A 128 REMARK 465 HIS A 129 REMARK 465 TYR A 130 REMARK 465 ASP A 131 REMARK 465 ARG A 132 REMARK 465 LEU A 133 REMARK 465 ARG A 134 REMARK 465 ASN A 135 REMARK 465 GLU A 136 REMARK 465 GLY A 137 REMARK 465 ARG A 290 REMARK 465 PRO A 291 REMARK 465 ASN A 292 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 GLN A 90 -60.80 71.20 REMARK 500 GLU A 193 -155.85 -171.32 REMARK 500 CYS A 194 -165.69 -111.40 REMARK 500 LEU A 212 44.64 -107.55 REMARK 500 ASP A 269 40.11 -97.40 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 PLP A 413 DBREF 1ET0 A 7 292 UNP P28305 PABC_ECOLI 1 269 SEQRES 1 A 269 MET PHE LEU ILE ASN GLY HIS LYS GLN GLU SER LEU ALA SEQRES 2 A 269 VAL SER ASP ARG ALA THR GLN PHE GLY ASP GLY CYS PHE SEQRES 3 A 269 THR THR ALA ARG VAL ILE ASP GLY LYS VAL SER LEU LEU SEQRES 4 A 269 SER ALA HIS ILE GLN ARG LEU GLN ASP ALA CYS GLN ARG SEQRES 5 A 269 LEU MET ILE SER CYS ASP PHE TRP PRO GLN LEU GLU GLN SEQRES 6 A 269 GLU MET LYS THR LEU ALA ALA GLU GLN GLN ASN GLY VAL SEQRES 7 A 269 LEU LYS VAL VAL ILE SER ARG GLY SER GLY GLY ARG GLY SEQRES 8 A 269 TYR SER THR LEU ASN SER GLY PRO ALA THR ARG ILE LEU SEQRES 9 A 269 SER VAL THR ALA TYR PRO ALA HIS TYR ASP ARG LEU ARG SEQRES 10 A 269 ASN GLU GLY ILE THR LEU ALA LEU SER PRO VAL ARG LEU SEQRES 11 A 269 GLY ARG ASN PRO HIS LEU ALA GLY ILE LYS HIS LEU ASN SEQRES 12 A 269 ARG LEU GLU GLN VAL LEU ILE ARG SER HIS LEU GLU GLN SEQRES 13 A 269 THR ASN ALA ASP GLU ALA LEU VAL LEU ASP SER GLU GLY SEQRES 14 A 269 TRP VAL THR GLU CYS CYS ALA ALA ASN LEU PHE TRP ARG SEQRES 15 A 269 LYS GLY ASN VAL VAL TYR THR PRO ARG LEU ASP GLN ALA SEQRES 16 A 269 GLY VAL ASN GLY ILE MET ARG GLN PHE CYS ILE ARG LEU SEQRES 17 A 269 LEU ALA GLN SER SER TYR GLN LEU VAL GLU VAL GLN ALA SEQRES 18 A 269 SER LEU GLU GLU SER LEU GLN ALA ASP GLU MET VAL ILE SEQRES 19 A 269 CYS ASN ALA LEU MET PRO VAL MET PRO VAL CYS ALA CYS SEQRES 20 A 269 GLY ASP VAL SER PHE SER SER ALA THR LEU TYR GLU TYR SEQRES 21 A 269 LEU ALA PRO LEU CYS GLU ARG PRO ASN HET PLP A 413 15 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 HOH *126(H2 O) HELIX 1 1 ASP A 26 GLY A 32 1 7 HELIX 2 2 LEU A 52 LEU A 67 1 16 HELIX 3 3 PHE A 74 GLN A 90 1 17 HELIX 4 4 ARG A 164 GLU A 175 1 12 HELIX 5 5 GLY A 219 SER A 232 1 14 HELIX 6 6 SER A 242 LEU A 247 1 6 HELIX 7 7 ALA A 278 GLU A 289 1 12 SHEET 1 A 6 HIS A 13 GLN A 15 0 SHEET 2 A 6 PHE A 8 ILE A 10 -1 O PHE A 8 N GLN A 15 SHEET 3 A 6 THR A 118 THR A 124 -1 N LEU A 121 O LEU A 9 SHEET 4 A 6 GLY A 94 SER A 101 -1 O VAL A 95 N THR A 124 SHEET 5 A 6 GLY A 34 ILE A 42 -1 N CYS A 35 O ILE A 100 SHEET 6 A 6 LYS A 49 VAL A 50 -1 O LYS A 49 N ILE A 42 SHEET 1 B 4 VAL A 191 GLU A 193 0 SHEET 2 B 4 GLU A 181 LEU A 185 -1 N VAL A 184 O GLU A 193 SHEET 3 B 4 THR A 140 LEU A 143 1 O THR A 140 N GLU A 181 SHEET 4 B 4 ALA A 266 CYS A 267 1 O ALA A 266 N LEU A 141 SHEET 1 C 5 GLN A 235 VAL A 239 0 SHEET 2 C 5 VAL A 206 PRO A 210 1 N VAL A 207 O GLN A 235 SHEET 3 C 5 ASN A 198 LYS A 203 -1 O TRP A 201 N TYR A 208 SHEET 4 C 5 GLU A 251 CYS A 255 -1 O GLU A 251 N ARG A 202 SHEET 5 C 5 VAL A 261 PRO A 263 -1 N MET A 262 O ILE A 254 LINK NZ LYS A 159 C4A PLP A 413 1555 1555 1.36 CISPEP 1 GLY A 115 PRO A 116 0 -0.12 CISPEP 2 MET A 259 PRO A 260 0 -0.55 SITE 1 AC1 14 ARG A 59 TYR A 109 LYS A 159 GLU A 193 SITE 2 AC1 14 CYS A 195 ALA A 196 ALA A 197 GLY A 219 SITE 3 AC1 14 ILE A 220 MET A 221 ASN A 256 ALA A 257 SITE 4 AC1 14 HOH A 529 HOH A 546 CRYST1 40.500 73.930 83.740 90.00 90.00 90.00 P 21 21 2 4 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 0.024690 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013530 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011940 0.00000