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 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 MASTER 252 0 1 8 20 0 5 6 0 0 0 21 END