HEADER ISOMERASE 11-APR-01 1IEZ TITLE SOLUTION STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE OF TITLE 2 RIBOFLAVIN BIOSYNTHESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHBP SYNTHASE, (DHBPS)S; COMPND 5 EC: 5.4.99.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE32 KEYWDS DIHYDROXYBUTANONE PHOSPHATE SYNTHASE, RIBOFLAVIN BIOSYNTHESIS, KEYWDS 2 SKELETAL REARRANGEMENT, ANTIMICROBIAL TARGET, STRUCTURE BASED KEYWDS 3 DESIGN, ISOMERASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.J.S.KELLY,L.J.BALL,R.KUHNE,A.BACHER,H.OSCHKINAT REVDAT 5 01-MAY-24 1IEZ 1 REMARK REVDAT 4 13-JUL-11 1IEZ 1 VERSN REVDAT 3 24-FEB-09 1IEZ 1 VERSN REVDAT 2 01-APR-03 1IEZ 1 JRNL REVDAT 1 07-NOV-01 1IEZ 0 JRNL AUTH M.J.KELLY,L.J.BALL,C.KRIEGER,Y.YU,M.FISCHER,S.SCHIFFMANN, JRNL AUTH 2 P.SCHMIEDER,R.KUHNE,W.BERMEL,A.BACHER,G.RICHTER,H.OSCHKINAT JRNL TITL THE NMR STRUCTURE OF THE 47-KDA DIMERIC ENZYME JRNL TITL 2 3,4-DIHYDROXY-2-BUTANONE-4-PHOSPHATE SYNTHASE AND LIGAND JRNL TITL 3 BINDING STUDIES REVEAL THE LOCATION OF THE ACTIVE SITE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 13025 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11687623 JRNL DOI 10.1073/PNAS.231323598 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ANSIG 3.0, X-PLOR 3.1 REMARK 3 AUTHORS : KRAULIS (ANSIG), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 730 NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 230 DIHEDRAL ANGLE RESTRAINTS, REMARK 3 40 DISTANCE RESTRAINTS FROM HYDROGEN BONDS REMARK 4 REMARK 4 1IEZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013221. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50MM NAPO4 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM DHBPS U-15N,13C, 50MMOL REMARK 210 NAPO4, PH 6, REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AZARA 3.3, X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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: MONOMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE A 45 H VAL A 171 1.49 REMARK 500 O ASP A 159 H LEU A 163 1.49 REMARK 500 O SER A 110 H ARG A 114 1.57 REMARK 500 O ARG A 114 H VAL A 118 1.58 REMARK 500 O THR A 154 H THR A 157 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 1 ASN A 2 56.41 -93.70 REMARK 500 1 SER A 7 -64.68 -92.18 REMARK 500 1 GLU A 25 41.98 -98.40 REMARK 500 1 ASP A 34 78.25 -109.77 REMARK 500 1 ASP A 36 -62.92 -96.31 REMARK 500 1 ASN A 39 -70.55 -173.28 REMARK 500 1 MET A 43 47.07 -93.88 REMARK 500 1 ILE A 44 20.52 -68.49 REMARK 500 1 MET A 50 86.08 -62.67 REMARK 500 1 ARG A 60 -64.07 -95.53 REMARK 500 1 LEU A 78 43.65 -97.74 REMARK 500 1 ASP A 79 76.65 -28.97 REMARK 500 1 MET A 82 46.01 -103.12 REMARK 500 1 GLU A 85 44.16 -101.48 REMARK 500 1 ASN A 86 81.05 -61.59 REMARK 500 1 THR A 88 -55.38 74.90 REMARK 500 1 TYR A 91 67.67 -68.18 REMARK 500 1 PHE A 95 100.14 -58.60 REMARK 500 1 THR A 96 81.05 -59.66 REMARK 500 1 VAL A 97 151.42 -33.48 REMARK 500 1 THR A 98 -178.37 -69.67 REMARK 500 1 ALA A 101 95.29 -51.37 REMARK 500 1 THR A 106 59.06 -145.91 REMARK 500 1 THR A 107 -31.97 -138.91 REMARK 500 1 ALA A 111 -29.85 -34.81 REMARK 500 1 ALA A 112 -74.86 -82.41 REMARK 500 1 ALA A 123 72.49 -106.58 REMARK 500 1 HIS A 136 38.22 31.21 REMARK 500 1 PRO A 168 84.46 -64.81 REMARK 500 1 GLU A 174 -169.06 -114.27 REMARK 500 1 LEU A 175 90.88 -63.67 REMARK 500 1 MET A 182 80.81 -63.83 REMARK 500 1 ALA A 185 160.02 60.85 REMARK 500 2 ASN A 2 55.83 -110.96 REMARK 500 2 SER A 8 38.98 -87.97 REMARK 500 2 PHE A 9 44.25 -67.26 REMARK 500 2 GLU A 25 42.76 -91.73 REMARK 500 2 ASP A 33 -61.90 -154.06 REMARK 500 2 ASP A 36 74.62 -167.82 REMARK 500 2 ARG A 37 -85.56 57.70 REMARK 500 2 ASN A 39 54.46 -108.43 REMARK 500 2 GLU A 40 127.01 -176.35 REMARK 500 2 MET A 43 53.92 -95.34 REMARK 500 2 ILE A 44 19.98 -61.22 REMARK 500 2 MET A 50 88.64 -51.53 REMARK 500 2 LEU A 78 44.55 -96.69 REMARK 500 2 ASP A 79 78.74 -26.81 REMARK 500 2 MET A 82 44.45 -99.63 REMARK 500 2 ASN A 86 82.15 -68.52 REMARK 500 2 ASN A 87 104.76 -43.11 REMARK 500 REMARK 500 THIS ENTRY HAS 349 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G57 RELATED DB: PDB REMARK 900 RELATED ID: 1G58 RELATED DB: PDB DBREF 1IEZ A 1 217 UNP P0A7J0 RIBB_ECOLI 1 217 SEQRES 1 A 217 MET ASN GLN THR LEU LEU SER SER PHE GLY THR PRO PHE SEQRES 2 A 217 GLU ARG VAL GLU ASN ALA LEU ALA ALA LEU ARG GLU GLY SEQRES 3 A 217 ARG GLY VAL MET VAL LEU ASP ASP GLU ASP ARG GLU ASN SEQRES 4 A 217 GLU GLY ASP MET ILE PHE PRO ALA GLU THR MET THR VAL SEQRES 5 A 217 GLU GLN MET ALA LEU THR ILE ARG HIS GLY SER GLY ILE SEQRES 6 A 217 VAL CYS LEU CYS ILE THR GLU ASP ARG ARG LYS GLN LEU SEQRES 7 A 217 ASP LEU PRO MET MET VAL GLU ASN ASN THR SER ALA TYR SEQRES 8 A 217 GLY THR GLY PHE THR VAL THR ILE GLU ALA ALA GLU GLY SEQRES 9 A 217 VAL THR THR GLY VAL SER ALA ALA ASP ARG ILE THR THR SEQRES 10 A 217 VAL ARG ALA ALA ILE ALA ASP GLY ALA LYS PRO SER ASP SEQRES 11 A 217 LEU ASN ARG PRO GLY HIS VAL PHE PRO LEU ARG ALA GLN SEQRES 12 A 217 ALA GLY GLY VAL LEU THR ARG GLY GLY HIS THR GLU ALA SEQRES 13 A 217 THR ILE ASP LEU MET THR LEU ALA GLY PHE LYS PRO ALA SEQRES 14 A 217 GLY VAL LEU CYS GLU LEU THR ASN ASP ASP GLY THR MET SEQRES 15 A 217 ALA ARG ALA PRO GLU CYS ILE GLU PHE ALA ASN LYS HIS SEQRES 16 A 217 ASN MET ALA LEU VAL THR ILE GLU ASP LEU VAL ALA TYR SEQRES 17 A 217 ARG GLN ALA HIS GLU ARG LYS ALA SER HELIX 1 1 PHE A 13 GLU A 25 1 13 HELIX 2 2 THR A 51 GLY A 62 1 12 HELIX 3 3 THR A 71 LEU A 78 1 8 HELIX 4 4 ALA A 112 ILE A 122 1 11 HELIX 5 5 THR A 154 LEU A 163 1 10 HELIX 6 6 ARG A 184 MET A 197 1 14 HELIX 7 7 ILE A 202 ARG A 214 1 13 SHEET 1 A 2 VAL A 29 LEU A 32 0 SHEET 2 A 2 ALA A 198 THR A 201 1 O ALA A 198 N MET A 30 SHEET 1 B 2 CYS A 67 ILE A 70 0 SHEET 2 B 2 PHE A 138 ARG A 141 1 O PHE A 138 N LEU A 68 CISPEP 1 ARG A 133 PRO A 134 1 8.06 CISPEP 2 ARG A 133 PRO A 134 2 7.20 CISPEP 3 ARG A 133 PRO A 134 3 7.92 CISPEP 4 ARG A 133 PRO A 134 4 8.69 CISPEP 5 ARG A 133 PRO A 134 5 7.02 CISPEP 6 ARG A 133 PRO A 134 6 1.90 CISPEP 7 ARG A 133 PRO A 134 7 -9.52 CISPEP 8 ARG A 133 PRO A 134 8 8.06 CISPEP 9 ARG A 133 PRO A 134 9 18.19 CISPEP 10 ARG A 133 PRO A 134 10 -8.72 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1