HEADER TRANSFERASE 28-NOV-05 2F65 TITLE SOLUTION STRUCTURE OF HPPK IN COMPLEX WITH INHIBITOR ANALOG AMPCPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE COMPND 3 PYROPHOSPHOKINASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, HPPK, COMPND 6 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK; COMPND 7 EC: 2.7.6.3; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: FOLK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS ALPHA-BETA-ALPHA FOLD, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR H.YAN,G.LI REVDAT 3 09-MAR-22 2F65 1 REMARK REVDAT 2 24-FEB-09 2F65 1 VERSN REVDAT 1 17-JAN-06 2F65 0 JRNL AUTH H.YAN,G.LI JRNL TITL SOLUTION STRUCTURE OF HPPK IN COMPLEX WITH INHIBITOR ANALOG JRNL TITL 2 AMPCPP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, ARIA 1.2 REMARK 3 AUTHORS : VARIAN (VNMR), LINGE (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 4273 STRUCTURALLY USEFUL REMARK 3 DISTANCE RESTRAINTS WERE USED FOR THE CALCULATION, OF WHICH 3069 REMARK 3 WERE UNAMBIGUOUS RESTRAINTS, 1204 AMBIGUOUS. TOTAL 47 H-BONDS REMARK 3 INCLUDED. REMARK 4 REMARK 4 2F65 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035498. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE,15MM REMARK 210 MGCL2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6 MM HPPK,U-15N,13C;20 MM REMARK 210 SODIUM PHOSPHATE,15MM MGCL2; REMARK 210 10MM AMPCPP; 0.05 MM DSS;5% D2O, REMARK 210 95%H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 5.0.4, CNS 1.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 HA VAL A 83 H GLU A 87 1.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 16 TYR A 40 CE1 TYR A 40 CZ 0.139 REMARK 500 16 TYR A 40 CZ TYR A 40 CE2 -0.144 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 SER A 9 151.21 75.11 REMARK 500 1 ASN A 10 -146.88 -159.75 REMARK 500 1 LEU A 11 143.52 72.53 REMARK 500 1 ALA A 12 -75.69 -3.41 REMARK 500 1 LYS A 23 -70.90 -65.28 REMARK 500 1 PRO A 29 -43.00 -25.33 REMARK 500 1 LEU A 34 -58.29 -124.18 REMARK 500 1 SER A 37 -163.54 -172.66 REMARK 500 1 SER A 38 67.39 66.67 REMARK 500 1 LEU A 45 71.60 52.12 REMARK 500 1 GLN A 48 -159.59 -144.77 REMARK 500 1 ASP A 52 -95.44 179.23 REMARK 500 1 TYR A 53 169.53 60.11 REMARK 500 1 LEU A 54 85.06 -163.88 REMARK 500 1 ALA A 65 153.42 -48.22 REMARK 500 1 PRO A 66 -19.85 -46.61 REMARK 500 1 GLN A 79 31.80 -153.11 REMARK 500 1 GLN A 80 -78.05 -139.68 REMARK 500 1 ARG A 82 -88.88 62.17 REMARK 500 1 VAL A 83 26.47 36.05 REMARK 500 1 LYS A 85 66.76 -174.12 REMARK 500 1 GLU A 87 6.87 46.86 REMARK 500 1 ARG A 88 -77.50 63.19 REMARK 500 1 TRP A 89 -164.99 -109.94 REMARK 500 1 PRO A 91 -176.00 -48.23 REMARK 500 1 ARG A 92 -158.85 67.45 REMARK 500 1 THR A 93 174.40 56.86 REMARK 500 1 ASP A 95 85.69 -154.06 REMARK 500 1 PHE A 101 71.22 -150.20 REMARK 500 1 ASN A 103 -4.21 72.92 REMARK 500 1 THR A 108 -94.67 -150.03 REMARK 500 1 GLU A 109 -49.58 -146.71 REMARK 500 1 THR A 112 98.80 -160.14 REMARK 500 1 HIS A 115 124.31 55.37 REMARK 500 1 ASN A 120 47.21 -97.10 REMARK 500 1 ARG A 121 63.49 -156.52 REMARK 500 1 PHE A 123 34.18 -98.45 REMARK 500 1 MET A 124 -34.31 -153.03 REMARK 500 1 ALA A 132 88.44 -174.43 REMARK 500 1 PRO A 133 45.69 -92.94 REMARK 500 1 VAL A 136 -77.81 37.45 REMARK 500 1 PHE A 137 -58.65 -14.43 REMARK 500 1 PRO A 138 -51.76 -24.52 REMARK 500 1 MET A 142 -149.12 -60.30 REMARK 500 1 ALA A 151 -101.03 -86.90 REMARK 500 1 PHE A 152 -134.60 -107.43 REMARK 500 1 ASP A 153 -30.26 -151.02 REMARK 500 1 LYS A 154 107.09 174.67 REMARK 500 2 ASN A 10 100.50 -161.48 REMARK 500 2 LEU A 11 -169.90 -160.02 REMARK 500 REMARK 500 THIS ENTRY HAS 799 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 6 TYR A 40 0.05 SIDE CHAIN REMARK 500 11 TYR A 40 0.07 SIDE CHAIN REMARK 500 12 TYR A 40 0.06 SIDE CHAIN REMARK 500 20 TYR A 4 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EQ0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AMPPCP REMARK 900 RELATED ID: 2F63 RELATED DB: PDB DBREF 2F65 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 HELIX 1 1 SER A 13 ASP A 27 1 15 HELIX 2 2 ALA A 65 LEU A 78 1 14 HELIX 3 3 ARG A 121 ALA A 132 1 12 HELIX 4 4 LEU A 143 ARG A 150 1 8 SHEET 1 A 2 ALA A 3 ALA A 6 0 SHEET 2 A 2 ASP A 97 PHE A 101 -1 O MET A 99 N TYR A 4 SHEET 1 B 2 ILE A 33 THR A 42 0 SHEET 2 B 2 ASP A 52 LEU A 60 -1 O ALA A 59 N THR A 35 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