PDB Short entry for 1I2K HEADER LYASE 09-FEB-01 1I2K TITLE AMINODEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-AMINO-4-DEOXYCHORISMATE LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.-.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PABC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE, PYRIDOXAL PHOSPHATE, AMINODEOXYCHORISMATE, PABC EXPDTA X-RAY DIFFRACTION AUTHOR P.Y.JENSEN,J.F.PARSONS,K.E.FISHER,A.S.PACHIKARA,M.TORDOVA,A.J.HOWARD, AUTHOR 2 E.EISENSTEIN,J.E.LADNER REVDAT 4 04-OCT-17 1I2K 1 REMARK REVDAT 3 13-JUL-11 1I2K 1 VERSN REVDAT 2 24-FEB-09 1I2K 1 VERSN REVDAT 1 02-SEP-03 1I2K 0 JRNL AUTH P.Y.JENSEN,J.F.PARSONS,K.E.FISHER,A.S.PACHIKARA,M.TORDOVA, JRNL AUTH 2 A.J.HOWARD,E.EISENSTEIN,J.E.LADNER JRNL TITL STRUCTURE AND MECHANISM OF ESCHERICHIA COLI JRNL TITL 2 AMINODEOXYCHORISMATE LYASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.163 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1153 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21637 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.159 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.160 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1115 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 20568 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2079 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2305.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 12 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9409 REMARK 3 NUMBER OF RESTRAINTS : 8766 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.038 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.045 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.008 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.079 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 115 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21637 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 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) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.36200 REMARK 200 R SYM FOR SHELL (I) : NULL 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: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE WATER MOLECULES HAVE BEEN ORDERED SO THAT THE FIRST REMARK 200 177 FORM THE FIRST HYDRATION SPHERE, THE NEXT 30 BELONG TO THE REMARK 200 SECOND HYDRATION SHPERE AND THE FINAL 5 BELONG TO THE THIRD REMARK 200 HYDRATION SHPERE. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.2M MAGNESIUM ACETATE, REMARK 280 0.1M HEPES, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 20.02350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.48300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.02350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.48300 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 300 REMARK: THE SECOND CHAIN IN THE DIMER IS GENERATED BY THE CRYSTAL REMARK 300 TWO FOLD: USE THE SYMMETRY -X,-Y,Z AND ADD ONE CELL IN X 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: 5610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 40.04700 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 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 519 LIES ON A SPECIAL POSITION. 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 75 -55.51 68.26 REMARK 500 GLU A 173 -166.94 -167.70 REMARK 500 CYS A 174 -160.96 -104.07 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 301 DBREF 1I2K A 1 269 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 301 15 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 HOH *212(H2 O) HELIX 1 1 ASP A 16 GLY A 22 1 7 HELIX 2 2 LEU A 38 LEU A 53 1 16 HELIX 3 3 PHE A 59 GLN A 75 1 17 HELIX 4 4 ALA A 111 GLY A 120 1 10 HELIX 5 5 ARG A 144 GLU A 155 1 12 HELIX 6 6 GLY A 199 SER A 212 1 14 HELIX 7 7 SER A 222 GLN A 228 1 7 HELIX 8 8 ALA A 255 ARG A 267 1 13 SHEET 1 A 6 HIS A 7 GLN A 9 0 SHEET 2 A 6 PHE A 2 ILE A 4 -1 O PHE A 2 N GLN A 9 SHEET 3 A 6 THR A 101 THR A 107 -1 N LEU A 104 O LEU A 3 SHEET 4 A 6 GLY A 77 SER A 84 -1 N VAL A 78 O THR A 107 SHEET 5 A 6 GLY A 24 ILE A 32 -1 O CYS A 25 N ILE A 83 SHEET 6 A 6 LYS A 35 VAL A 36 -1 O LYS A 35 N ILE A 32 SHEET 1 B 8 GLN A 215 VAL A 219 0 SHEET 2 B 8 VAL A 186 PRO A 190 1 N VAL A 187 O GLN A 215 SHEET 3 B 8 ASN A 178 LYS A 183 -1 O TRP A 181 N TYR A 188 SHEET 4 B 8 GLU A 231 CYS A 235 -1 O GLU A 231 N ARG A 182 SHEET 5 B 8 VAL A 241 CYS A 247 -1 N MET A 242 O ILE A 234 SHEET 6 B 8 ILE A 121 LEU A 125 1 N ILE A 121 O PRO A 243 SHEET 7 B 8 GLU A 161 LEU A 165 1 N GLU A 161 O THR A 122 SHEET 8 B 8 VAL A 171 GLU A 173 -1 N THR A 172 O VAL A 164 SHEET 1 C 6 GLN A 215 VAL A 219 0 SHEET 2 C 6 VAL A 186 PRO A 190 1 N VAL A 187 O GLN A 215 SHEET 3 C 6 ASN A 178 LYS A 183 -1 O TRP A 181 N TYR A 188 SHEET 4 C 6 GLU A 231 CYS A 235 -1 O GLU A 231 N ARG A 182 SHEET 5 C 6 VAL A 241 CYS A 247 -1 N MET A 242 O ILE A 234 SHEET 6 C 6 VAL A 250 SER A 251 -1 O VAL A 250 N CYS A 247 LINK C4A PLP A 301 NZ LYS A 140 1555 1555 1.36 CISPEP 1 GLY A 98 PRO A 99 0 8.30 CISPEP 2 MET A 239 PRO A 240 0 -1.88 CISPEP 3 ARG A 267 PRO A 268 0 -1.31 SITE 1 AC1 17 ARG A 45 TYR A 92 LYS A 140 GLU A 173 SITE 2 AC1 17 CYS A 175 ALA A 176 ALA A 177 ASN A 178 SITE 3 AC1 17 VAL A 197 GLY A 199 ILE A 200 MET A 201 SITE 4 AC1 17 ASN A 236 ALA A 237 HOH A 413 HOH A 576 SITE 5 AC1 17 HOH A 577 CRYST1 40.047 72.966 82.871 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 0.024971 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012067 0.00000