HEADER ISOMERASE 24-OCT-02 1N2U OBSLTE 26-AUG-03 1N2U 1Q54 TITLE STRUCTURE AND MECHANISM OF ACTION OF TITLE 2 ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE TITLE 3 ISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOPENTENYL DIPHOSPHATE DELTA-ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DIMETHYLALLYL DIPHOSPHATE ISOMERASE, IPP COMPND 5 ISOMERASE, ISOPENTENYL PYROPHOSPHATE ISOMERASE; COMPND 6 EC: 5.3.3.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PYL20 KEYWDS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.WOUTERS,Y.OUDJAMA,S.GHOSH,V.STALON,L.DROOGMANS,E.OLDFIELD REVDAT 3 26-AUG-03 1N2U 2 OBSLTE REVDAT 2 01-APR-03 1N2U 1 AUTHOR REVDAT 1 18-MAR-03 1N2U 0 JRNL AUTH J.WOUTERS,Y.OUDJAMA,S.GHOSH,V.STALON,L.DROOGMANS, JRNL AUTH 2 E.OLDFIELD JRNL TITL STRUCTURE AND MECHANISM OF ACTION OF JRNL TITL 2 ISOPENTENYLPYROPHOSPHATE- JRNL TITL 3 DIMETHYLALLYLPYROPHOSPHATE ISOMERASE JRNL REF J.AM.CHEM.SOC. V. 125 3198 2003 JRNL REFN ASTM JACSAT US ISSN 0002-7863 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.93 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.210 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.210 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3212 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 29014 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.201 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2959 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 26583 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2819 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3029.63 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 3 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 12257 REMARK 3 NUMBER OF RESTRAINTS : 15465 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.050 REMARK 3 ANGLE DISTANCES (A) : 0.049 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.051 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.030 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.031 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.102 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.049 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 1N2U COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-2002. REMARK 100 THE RCSB ID CODE IS RCSB017448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-2000 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR RESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MARFLM REMARK 200 DATA SCALING SOFTWARE : MARFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.12800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 1HZT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, MANGANESE CHLORIDE, REMARK 280 AMMONIUM SULFATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 34.41500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.74500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.67500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.74500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.67500 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 GLN A 2 REMARK 465 THR A 3 REMARK 465 GLN A 180 REMARK 465 LEU A 181 REMARK 465 LYS A 182 REMARK 465 LEU A 183 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 THR B 3 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 REMARK 500 MG MG A 401 O8 BHI 301 0.97 REMARK 500 BR BHI 301 O HOH 501 1.47 REMARK 500 MG MG B 401 O8 BHI 302 1.60 REMARK 500 MG MG A 401 O4 BHI 301 1.65 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HZT RELATED DB: PDB REMARK 900 UNCOMPLEXED PROTEIN REMARK 900 RELATED ID: 1HX3 RELATED DB: PDB REMARK 900 METAL BOUND PROTEIN DBREF 1N2U A 1 182 UNP Q46822 IDI_ECOLI 1 182 DBREF 1N2U B 1 182 UNP Q46822 IDI_ECOLI 1 182 SEQADV 1N2U ALA A 67 UNP Q46822 CYS 67 ENGINEERED SEQADV 1N2U LEU A 183 UNP Q46822 CLONING ARTIFACT SEQADV 1N2U ALA B 67 UNP Q46822 CYS 67 ENGINEERED SEQADV 1N2U LEU B 183 UNP Q46822 CLONING ARTIFACT SEQRES 1 A 183 MET GLN THR GLU HIS VAL ILE LEU LEU ASN ALA GLN GLY SEQRES 2 A 183 VAL PRO THR GLY THR LEU GLU LYS TYR ALA ALA HIS THR SEQRES 3 A 183 ALA ASP THR ARG LEU HIS LEU ALA PHE SER SER TRP LEU SEQRES 4 A 183 PHE ASN ALA LYS GLY GLN LEU LEU VAL THR ARG ARG ALA SEQRES 5 A 183 LEU SER LYS LYS ALA TRP PRO GLY VAL TRP THR ASN SER SEQRES 6 A 183 VAL ALA GLY HIS PRO GLN LEU GLY GLU SER ASN GLU ASP SEQRES 7 A 183 ALA VAL ILE ARG ARG CYS ARG TYR GLU LEU GLY VAL GLU SEQRES 8 A 183 ILE THR PRO PRO GLU SER ILE TYR PRO ASP PHE ARG TYR SEQRES 9 A 183 ARG ALA THR ASP PRO SER GLY ILE VAL GLU ASN GLU VAL SEQRES 10 A 183 CYS PRO VAL PHE ALA ALA ARG THR THR SER ALA LEU GLN SEQRES 11 A 183 ILE ASN ASP ASP GLU VAL MET ASP TYR GLN TRP CYS ASP SEQRES 12 A 183 LEU ALA ASP VAL LEU HIS GLY ILE ASP ALA THR PRO TRP SEQRES 13 A 183 ALA PHE SER PRO TRP MET VAL MET GLN ALA THR ASN ARG SEQRES 14 A 183 GLU ALA ARG LYS ARG LEU SER ALA PHE THR GLN LEU LYS SEQRES 15 A 183 LEU SEQRES 1 B 183 MET GLN THR GLU HIS VAL ILE LEU LEU ASN ALA GLN GLY SEQRES 2 B 183 VAL PRO THR GLY THR LEU GLU LYS TYR ALA ALA HIS THR SEQRES 3 B 183 ALA ASP THR ARG LEU HIS LEU ALA PHE SER SER TRP LEU SEQRES 4 B 183 PHE ASN ALA LYS GLY GLN LEU LEU VAL THR ARG ARG ALA SEQRES 5 B 183 LEU SER LYS LYS ALA TRP PRO GLY VAL TRP THR ASN SER SEQRES 6 B 183 VAL ALA GLY HIS PRO GLN LEU GLY GLU SER ASN GLU ASP SEQRES 7 B 183 ALA VAL ILE ARG ARG CYS ARG TYR GLU LEU GLY VAL GLU SEQRES 8 B 183 ILE THR PRO PRO GLU SER ILE TYR PRO ASP PHE ARG TYR SEQRES 9 B 183 ARG ALA THR ASP PRO SER GLY ILE VAL GLU ASN GLU VAL SEQRES 10 B 183 CYS PRO VAL PHE ALA ALA ARG THR THR SER ALA LEU GLN SEQRES 11 B 183 ILE ASN ASP ASP GLU VAL MET ASP TYR GLN TRP CYS ASP SEQRES 12 B 183 LEU ALA ASP VAL LEU HIS GLY ILE ASP ALA THR PRO TRP SEQRES 13 B 183 ALA PHE SER PRO TRP MET VAL MET GLN ALA THR ASN ARG SEQRES 14 B 183 GLU ALA ARG LYS ARG LEU SER ALA PHE THR GLN LEU LYS SEQRES 15 B 183 LEU HET MN A 201 1 HET MN B 201 1 HET MG A 401 1 HET MG B 401 1 HET BHI 301 32 HET BHI 302 32 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM BHI 4-BROMO-3-HYDROXY-3-METHYL BUTYL DIPHOSPHATE FORMUL 3 MN 2(MN 2+) FORMUL 5 MG 2(MG 2+) FORMUL 7 BHI 2(C5 H13 BR O8 P2) FORMUL 9 HOH *175(H2 O1) HELIX 1 1 LYS A 21 HIS A 25 1 5 HELIX 2 2 SER A 75 GLY A 89 1 15 HELIX 3 3 ASP A 143 THR A 154 1 12 HELIX 4 4 PRO A 155 PHE A 158 5 4 HELIX 5 5 SER A 159 ASN A 168 1 10 HELIX 6 6 ASN A 168 THR A 179 1 12 HELIX 7 7 LYS B 21 HIS B 25 1 5 HELIX 8 8 SER B 75 GLY B 89 1 15 HELIX 9 9 ASP B 143 THR B 154 1 12 HELIX 10 10 PRO B 155 PHE B 158 5 4 HELIX 11 11 SER B 159 ASN B 168 1 10 HELIX 12 12 ASN B 168 PHE B 178 1 11 SHEET 1 A 2 HIS A 5 LEU A 9 0 SHEET 2 A 2 PRO A 15 GLU A 20 -1 N THR A 16 O LEU A 8 SHEET 1 B 3 HIS A 32 LEU A 33 0 SHEET 2 B 3 VAL A 113 VAL A 117 1 O ASN A 115 N HIS A 32 SHEET 3 B 3 ARG A 103 THR A 107 -1 N TYR A 104 O GLU A 116 SHEET 1 C 9 VAL A 136 CYS A 142 0 SHEET 2 C 9 LEU A 46 ARG A 51 -1 N LEU A 46 O CYS A 142 SHEET 3 C 9 TRP A 62 THR A 63 -1 N THR A 63 O THR A 49 SHEET 4 C 9 LEU A 46 ARG A 51 -1 O THR A 49 N THR A 63 SHEET 5 C 9 PHE A 35 PHE A 40 -1 O LEU A 39 N LEU A 47 SHEET 6 C 9 VAL A 66 GLY A 68 -1 O VAL A 66 N SER A 37 SHEET 7 C 9 PHE A 35 PHE A 40 -1 N PHE A 35 O GLY A 68 SHEET 8 C 9 VAL A 120 ARG A 124 1 N PHE A 121 O SER A 36 SHEET 9 C 9 GLU A 96 TYR A 99 -1 N GLU A 96 O ALA A 122 SHEET 1 D 2 HIS B 5 LEU B 9 0 SHEET 2 D 2 PRO B 15 GLU B 20 -1 N THR B 16 O LEU B 8 SHEET 1 E 3 HIS B 32 LEU B 33 0 SHEET 2 E 3 VAL B 113 VAL B 117 1 O ASN B 115 N HIS B 32 SHEET 3 E 3 ARG B 103 THR B 107 -1 O TYR B 104 N GLU B 116 SHEET 1 F 4 GLU B 96 TYR B 99 0 SHEET 2 F 4 VAL B 120 ARG B 124 -1 O VAL B 120 N ILE B 98 SHEET 3 F 4 PHE B 35 PHE B 40 1 O SER B 36 N PHE B 121 SHEET 4 F 4 VAL B 66 GLY B 68 -1 O VAL B 66 N SER B 37 CRYST1 68.830 71.350 91.490 90.00 90.00 90.00 P 21 21 21 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 0.014529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010930 0.00000