HEADER TRANSFERASE 05-APR-00 1EQO OBSLTE 26-AUG-03 1EQO 1Q0N TITLE CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF 6-HYDROXYMETHYL-7, TITLE 2 8-DIHYDROPTERIN PYROPHOSPHOKINASE FROM E. COLI WITH TITLE 3 MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.25 TITLE 4 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN COMPND 3 PYROPHOSPHOKINASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: HPPK; COMPND 6 EC: 2.7.6.3; COMPND 7 ENGINEERED: 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_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS PYROPHOSPHOKINASE, PYROPHOSPHORYL TRANSFER, FOLATE, HPPK, KEYWDS 2 PTERIN, 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN, TERNARY COMPLEX, KEYWDS 3 SUBSTRATE SPECIFICITY, ANTIMICROBIAL AGENT, DRUG DESIGN, X- KEYWDS 4 RAY CRYSTALLOGRAPHY EXPDTA X-RAY DIFFRACTION AUTHOR J.BLASZCZYK,X.JI REVDAT 2 26-AUG-03 1EQO 1 OBSLTE REVDAT 1 25-OCT-00 1EQO 0 JRNL AUTH J.BLASZCZYK,G.SHI,H.YAN,X.JI JRNL TITL CATALYTIC CENTER ASSEMBLY OF HPPK AS REVEALED BY JRNL TITL 2 THE CRYSTAL STRUCTURE OF A TERNARY COMPLEX AT 1.25 JRNL TITL 3 A RESOLUTION. JRNL REF STRUCTURE FOLD.DES. V. 8 1049 2000 JRNL REFN ASTM FODEFH UK ISSN 0969-2126 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.XIAO,G.SHI,X.CHEN,H.YAN,X.JI REMARK 1 TITL CRYSTAL STRUCTURE OF REMARK 1 TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN REMARK 1 TITL 3 PYROPHOSPHOKINASE, A POTENTIAL TARGET FOR THE REMARK 1 TITL 4 DEVELOPMENT OF NOVEL ANTIMICROBIAL AGENTS REMARK 1 REF STRUCTURE (LONDON) V. 7 489 1999 REMARK 1 REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.114 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.114 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1894 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 37078 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)) : 0.095 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.235 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1592 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 30413 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1296 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 343 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1664.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1296.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14405 REMARK 3 NUMBER OF RESTRAINTS : 17537 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.156 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.166 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.225 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.019 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.087 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-202 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FULL-MATRIX LEAST-SQUARES PROCEDURE, REMARK 3 WITH BLOCK OF PARAMETERS SET FOR EACH CYCLE OF REFINEMENT REMARK 4 REMARK 4 1EQO COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-2000. REMARK 100 THE RCSB ID CODE IS RCSB010825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-1999 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92000 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM-4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38972 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.156 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1HKA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, MAGNESIUM CHLORIDE, REMARK 280 ACETATE, GLYCEROL , PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 1/2+X,1/2+Y,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 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 36.79550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.87150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.79550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.87150 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 1 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 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 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 C ACT 167 LIES ON A SPECIAL POSITION. REMARK 375 HOH 406 LIES ON A SPECIAL POSITION. REMARK 375 HOH 414 LIES ON A SPECIAL POSITION. REMARK 375 HOH 472 LIES ON A SPECIAL POSITION. REMARK 375 HOH 541 LIES ON A SPECIAL POSITION. REMARK 375 HOH 542 LIES ON A SPECIAL POSITION. 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 CE MET A 142 OE1 GLN A 145 1.24 REMARK 500 O HOH 309 O HOH 383 1.65 REMARK 500 O HOH 382 O HOH 543 1.67 REMARK 500 O HOH 299 O HOH 300 1.70 REMARK 500 O HOH 489 O HOH 539 2.13 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HKA RELATED DB: PDB REMARK 900 1HKA IS THE CRYSTAL STRUCTURE OF UNLIGANDED HPPK FROM E. REMARK 900 COLI. REMARK 900 RELATED ID: 1EQM RELATED DB: PDB REMARK 900 1EQM IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK REMARK 900 FROM E. COLI WITH MGADP. REMARK 900 RELATED ID: 1EQ0 RELATED DB: PDB REMARK 900 1EQ0 IS THE SOLUTION STRUCTURE OF BINARY COMPLEX OF HPPK REMARK 900 FROM E. COLI WITH MGAMPPCP. REMARK 900 RELATED ID: 1CBK RELATED DB: PDB REMARK 900 1CBK IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK REMARK 900 FROM HAEMOPHILUS INFLUENZAE WITH A 6-HYDROXYMETHYL-7,8- REMARK 900 DIHYDROPTERIN ANALOG. REMARK 900 RELATED ID: 1DY3 RELATED DB: PDB REMARK 900 1DY3 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK REMARK 900 FROM E. COLI WITH MGATP AND A 6-HYDROXYMETHYL-7,8- REMARK 900 DIHYDROPTERIN ANALOG. DBREF 1EQO A 1 158 UNP P26281 HPPK_ECOLI 1 158 SEQRES 1 A 158 THR VAL ALA TYR ILE ALA ILE GLY SER ASN LEU ALA SER SEQRES 2 A 158 PRO LEU GLU GLN VAL ASN ALA ALA LEU LYS ALA LEU GLY SEQRES 3 A 158 ASP ILE PRO GLU SER HIS ILE LEU THR VAL SER SER PHE SEQRES 4 A 158 TYR ARG THR PRO PRO LEU GLY PRO GLN ASP GLN PRO ASP SEQRES 5 A 158 TYR LEU ASN ALA ALA VAL ALA LEU GLU THR SER LEU ALA SEQRES 6 A 158 PRO GLU GLU LEU LEU ASN HIS THR GLN ARG ILE GLU LEU SEQRES 7 A 158 GLN GLN GLY ARG VAL ARG LYS ALA GLU ARG TRP GLY PRO SEQRES 8 A 158 ARG THR LEU ASP LEU ASP ILE MET LEU PHE GLY ASN GLU SEQRES 9 A 158 VAL ILE ASN THR GLU ARG LEU THR VAL PRO HIS TYR ASP SEQRES 10 A 158 MET LYS ASN ARG GLY PHE MET LEU TRP PRO LEU PHE GLU SEQRES 11 A 158 ILE ALA PRO GLU LEU VAL PHE PRO ASP GLY GLU MET LEU SEQRES 12 A 158 ARG GLN ILE LEU HIS THR ARG ALA PHE ASP LYS LEU ASN SEQRES 13 A 158 LYS TRP HET MG A 161 1 HET MG A 162 1 HET CL 163 1 HET ACT 164 4 HET ACT 165 4 HET ACT 166 4 HET ACT 167 4 HET APC 171 31 HET HHP 181 14 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM HHP 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE FORMUL 2 MG 2(MG 2+) FORMUL 4 CL CL 1- FORMUL 5 ACT 4(C2 H3 O2 1-) FORMUL 9 APC C11 H18 N5 O12 P3 FORMUL 10 HHP C7 H9 N5 O2 FORMUL 11 HOH *343(H2 O1) HELIX 1 1 SER A 13 ASP A 27 1 15 HELIX 2 2 ALA A 65 GLN A 80 1 16 HELIX 3 3 ASP A 117 ASN A 120 5 4 HELIX 4 4 ARG A 121 ALA A 132 1 12 HELIX 5 5 MET A 142 ALA A 151 1 10 SHEET 1 A 4 ASP A 95 PHE A 101 0 SHEET 2 A 4 VAL A 2 SER A 9 -1 N TYR A 4 O LEU A 100 SHEET 3 A 4 TYR A 53 THR A 62 -1 N LEU A 54 O SER A 9 SHEET 4 A 4 SER A 31 VAL A 36 -1 O HIS A 32 N GLU A 61 SHEET 1 B 5 ASP A 95 PHE A 101 0 SHEET 2 B 5 VAL A 2 SER A 9 -1 N TYR A 4 O LEU A 100 SHEET 3 B 5 TYR A 53 THR A 62 -1 N LEU A 54 O SER A 9 SHEET 4 B 5 TYR A 40 THR A 42 -1 N TYR A 40 O ASN A 55 SHEET 5 B 5 ASN A 156 LYS A 157 -1 O ASN A 156 N ARG A 41 SHEET 1 C 2 ILE A 106 ASN A 107 0 SHEET 2 C 2 THR A 112 VAL A 113 -1 O VAL A 113 N ILE A 106 CISPEP 1 VAL A 113 PRO A 114 0 -9.50 CRYST1 73.591 37.743 57.909 90.00 116.94 90.00 C 1 2 1 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 0.013589 0.000000 0.006906 0.00000 SCALE2 0.000000 0.026495 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019371 0.00000