HEADER LYASE 09-FEB-01 1I2L TITLE DEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI WITH INHIBITOR 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, D-CYCLOSERINE 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 6 03-APR-24 1I2L 1 REMARK REVDAT 5 07-FEB-24 1I2L 1 REMARK REVDAT 4 04-OCT-17 1I2L 1 REMARK REVDAT 3 13-JUL-11 1I2L 1 VERSN REVDAT 2 24-FEB-09 1I2L 1 VERSN REVDAT 1 02-SEP-03 1I2L 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. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.00 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) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 9900 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 542 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 : 2079 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 142 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) : 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1I2L 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_1000012824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-00 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) : 0.98790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10442 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.21700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: ADC LYASE REMARK 200 REMARK 200 REMARK: THE WATER MOLECULES HAVE BEEN ORDERED SO THAT THOSE THAT REMARK 200 AGREE WITHIN 1.0 A OF WATER MOLECULES IN THE ADC LYASE 1.8 A REMARK 200 STRUCTURE WITHOUT AN INHIBITOR ARE NUMBERED THE SAME. OTHER REMARK 200 WATER MOLECULES ARE NUMBERED STARTING WITH 801. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.01 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 19.74700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.03000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.74700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.03000 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: 5810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 39.49400 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 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 PHE A 21 11.33 -141.09 REMARK 500 GLN A 75 -54.12 73.31 REMARK 500 PRO A 110 158.87 -49.11 REMARK 500 ASN A 118 30.92 -92.69 REMARK 500 GLU A 119 -14.04 -156.27 REMARK 500 ASN A 133 93.21 -164.24 REMARK 500 GLU A 173 -154.16 -170.63 REMARK 500 ALA A 255 22.95 -151.73 REMARK 500 PRO A 268 -174.93 -68.52 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 DCS A 301 DBREF 1I2L 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 DCS A 301 22 HETNAM DCS D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4- HETNAM 2 DCS YLMETHYL]-N,O-CYCLOSERYLAMIDE HETSYN DCS D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE FORMUL 2 DCS C11 H16 N3 O7 P FORMUL 3 HOH *142(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 ASN A 118 1 8 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 LEU A 227 1 6 HELIX 8 8 ALA A 255 GLU A 266 1 12 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 O LEU A 104 N 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 O ILE A 121 N CYS A 245 SHEET 7 B 8 GLU A 161 LEU A 165 1 O GLU A 161 N ALA A 124 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 N VAL A 250 O CYS A 247 CISPEP 1 GLY A 98 PRO A 99 0 0.16 CISPEP 2 MET A 239 PRO A 240 0 -0.22 SITE 1 AC1 17 ARG A 45 TYR A 92 LYS A 140 GLN A 147 SITE 2 AC1 17 GLU A 173 CYS A 175 ALA A 176 ALA A 177 SITE 3 AC1 17 ASN A 178 VAL A 197 GLY A 199 ILE A 200 SITE 4 AC1 17 MET A 201 ASN A 236 ALA A 237 HOH A 413 SITE 5 AC1 17 HOH A 577 CRYST1 39.494 72.060 81.662 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 0.025320 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012246 0.00000