PDB Short entry for 1JKN HEADER HYDROLASE 12-JUL-01 1JKN TITLE SOLUTION STRUCTURE OF THE NUDIX ENZYME DIADENOSINE TETRAPHOSPHATE TITLE 2 HYDROLASE FROM LUPINUS ANGUSTIFOLIUS COMPLEXED WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LUPINUS ANGUSTIFOLIUS; SOURCE 3 ORGANISM_COMMON: NARROW-LEAVED BLUE LUPINE; SOURCE 4 ORGANISM_TAXID: 3871; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-3 KEYWDS ALPHA-BETA-ALPHA SANDWICH, ENZYME-SUBSTRATE COMPLEX, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR J.I.FLETCHER,J.D.SWARBRICK,D.MAKSEL,K.R.GAYLER,P.R.GOOLEY REVDAT 4 23-FEB-22 1JKN 1 REMARK SEQADV REVDAT 3 24-FEB-09 1JKN 1 VERSN REVDAT 2 01-APR-03 1JKN 1 JRNL REVDAT 1 27-FEB-02 1JKN 0 JRNL AUTH J.I.FLETCHER,J.D.SWARBRICK,D.MAKSEL,K.R.GAYLER,P.R.GOOLEY JRNL TITL THE STRUCTURE OF AP(4)A HYDROLASE COMPLEXED WITH ATP-MGF(X) JRNL TITL 2 REVEALS THE BASIS OF SUBSTRATE BINDING. JRNL REF STRUCTURE V. 10 205 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 11839306 JRNL DOI 10.1016/S0969-2126(02)00696-2 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.D.SWARBRICK,T.BASHTANNYK,D.MAKSEL,X.-R.ZHANG, REMARK 1 AUTH 2 G.M.BLACKBURN,K.R.GAYLER,P.R.GOOLEY REMARK 1 TITL THE THREE-DIMENSIONAL STRUCTURE OF THE NUDIX ENZYME REMARK 1 TITL 2 DIADENOSINE TETRAPHOSPHATE HYDROLASE FROM LUPINUS REMARK 1 TITL 3 ANGUSTIFOLIUS L REMARK 1 REF J.MOL.BIOL. V. 302 1165 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.2000.4085 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.2, DYANA 1.5, CNS 1.0 REMARK 3 AUTHORS : VARIAN (VNMR), GUENTERT, ET AL. (DYANA), BRUNGER REMARK 3 ET AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 2948 RESTRAINTS. 2649 ARE NOE-BASED DISTANCE RESTRAINTS, 299 ARE REMARK 3 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1JKN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013881. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 120 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6 MM U-15N, U-13C AP4A REMARK 210 HYDROLASE 1.6 MM ATP 20 MM U-100% REMARK 210 2H IMIDAZOLE 32 MM NAF 20 MM REMARK 210 MGCL2; 1.6 MM U-15N, U-13C AP4A REMARK 210 HYDROLASE 1.6 MM ATP 20 MM U-100% REMARK 210 2H IMIDAZOLE 32 MM NAF 20 MM REMARK 210 MGCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNHA; 3D_15N-SEPARATED_NOESY; REMARK 210 3D_13C-SEPARATED_NOESY; 2D_DOUBLY-TUNED_13C_15N-FILTERED_NOESY; REMARK 210 13C-EDITED_13C-FILTERED_NOESY-HSQC 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 1.1, XEASY 1.4 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY, STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT VIOLATIONS, REMARK 210 TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 21 REMARK 210 REMARK 210 REMARK: DETERMINED USING STANDARD HETERONUCLEAR TECHNIQUES 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 CYS A 20 H PHE A 110 1.55 REMARK 500 O VAL A 88 H LEU A 92 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 MET A 6 111.97 -174.88 REMARK 500 1 SER A 8 137.50 -177.61 REMARK 500 1 LYS A 26 24.86 80.99 REMARK 500 1 PHE A 29 107.97 -59.75 REMARK 500 1 ILE A 47 159.63 51.95 REMARK 500 1 GLU A 49 99.28 -55.59 REMARK 500 1 ASP A 99 75.45 -112.89 REMARK 500 1 ASP A 124 38.74 -92.88 REMARK 500 2 SER A 5 121.71 -171.06 REMARK 500 2 SER A 8 130.73 174.64 REMARK 500 2 LYS A 26 24.77 81.74 REMARK 500 2 PHE A 29 109.58 -57.79 REMARK 500 2 ASP A 99 64.22 -109.75 REMARK 500 2 ASP A 124 38.72 -91.76 REMARK 500 3 SER A 5 -155.59 -108.08 REMARK 500 3 MET A 6 -40.33 -148.07 REMARK 500 3 SER A 8 131.70 171.88 REMARK 500 3 PHE A 29 108.61 -53.71 REMARK 500 3 GLU A 49 98.07 -55.19 REMARK 500 3 ASP A 116 -17.49 -48.97 REMARK 500 3 ASP A 124 38.83 -93.92 REMARK 500 3 SER A 126 -62.34 -102.24 REMARK 500 3 PRO A 129 -176.87 -51.69 REMARK 500 3 GLU A 130 -41.97 -150.10 REMARK 500 3 LYS A 150 16.28 -145.99 REMARK 500 4 LEU A 3 -178.53 60.18 REMARK 500 4 SER A 5 124.37 -173.14 REMARK 500 4 MET A 6 -38.31 -133.04 REMARK 500 4 SER A 8 138.98 174.33 REMARK 500 4 PHE A 29 109.58 -56.45 REMARK 500 4 GLU A 49 98.09 -53.60 REMARK 500 4 ASP A 99 65.23 -109.75 REMARK 500 4 ASP A 116 -16.69 -49.85 REMARK 500 4 ASP A 124 38.96 -93.75 REMARK 500 4 SER A 126 -68.28 -121.36 REMARK 500 4 PRO A 129 165.34 -48.44 REMARK 500 4 GLU A 130 -45.68 -150.05 REMARK 500 5 SER A 5 125.66 -179.57 REMARK 500 5 MET A 6 -24.70 -150.89 REMARK 500 5 ASP A 7 43.31 77.57 REMARK 500 5 SER A 8 121.54 -177.85 REMARK 500 5 GLU A 49 98.74 -67.26 REMARK 500 5 ASP A 99 73.82 -108.34 REMARK 500 5 ASP A 124 38.97 -91.98 REMARK 500 5 SER A 126 -69.96 -121.15 REMARK 500 6 PRO A 2 -168.73 -69.89 REMARK 500 6 LEU A 3 124.64 63.41 REMARK 500 6 SER A 5 -156.72 -124.13 REMARK 500 6 MET A 6 -33.65 -142.66 REMARK 500 6 SER A 8 125.64 178.24 REMARK 500 REMARK 500 THIS ENTRY HAS 256 RAMACHANDRAN OUTLIERS. 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 ATP A 166 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F3Y RELATED DB: PDB REMARK 900 1F3Y CONTAINS THE SAME PROTEIN IN THE FREE FORM DBREF 1JKN A 6 165 UNP O04841 O04841_LUPAN 40 199 SEQADV 1JKN GLY A 1 UNP O04841 CLONING ARTIFACT SEQADV 1JKN PRO A 2 UNP O04841 CLONING ARTIFACT SEQADV 1JKN LEU A 3 UNP O04841 CLONING ARTIFACT SEQADV 1JKN GLY A 4 UNP O04841 CLONING ARTIFACT SEQADV 1JKN SER A 5 UNP O04841 CLONING ARTIFACT SEQRES 1 A 165 GLY PRO LEU GLY SER MET ASP SER PRO PRO GLU GLY TYR SEQRES 2 A 165 ARG ARG ASN VAL GLY ILE CYS LEU MET ASN ASN ASP LYS SEQRES 3 A 165 LYS ILE PHE ALA ALA SER ARG LEU ASP ILE PRO ASP ALA SEQRES 4 A 165 TRP GLN MET PRO GLN GLY GLY ILE ASP GLU GLY GLU ASP SEQRES 5 A 165 PRO ARG ASN ALA ALA ILE ARG GLU LEU ARG GLU GLU THR SEQRES 6 A 165 GLY VAL THR SER ALA GLU VAL ILE ALA GLU VAL PRO TYR SEQRES 7 A 165 TRP LEU THR TYR ASP PHE PRO PRO LYS VAL ARG GLU LYS SEQRES 8 A 165 LEU ASN ILE GLN TRP GLY SER ASP TRP LYS GLY GLN ALA SEQRES 9 A 165 GLN LYS TRP PHE LEU PHE LYS PHE THR GLY GLN ASP GLN SEQRES 10 A 165 GLU ILE ASN LEU LEU GLY ASP GLY SER GLU LYS PRO GLU SEQRES 11 A 165 PHE GLY GLU TRP SER TRP VAL THR PRO GLU GLN LEU ILE SEQRES 12 A 165 ASP LEU THR VAL GLU PHE LYS LYS PRO VAL TYR LYS GLU SEQRES 13 A 165 VAL LEU SER VAL PHE ALA PRO HIS LEU HET ATP A 166 43 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ATP C10 H16 N5 O13 P3 HELIX 1 1 ASP A 52 THR A 65 1 14 HELIX 2 2 PRO A 85 TRP A 96 1 12 HELIX 3 3 GLU A 140 THR A 146 1 7 HELIX 4 4 VAL A 147 PHE A 149 5 3 HELIX 5 5 LYS A 150 PHE A 161 1 12 HELIX 6 6 ALA A 162 LEU A 165 5 4 SHEET 1 A 4 ALA A 70 GLU A 75 0 SHEET 2 A 4 PHE A 108 PHE A 112 -1 N LEU A 109 O ALA A 74 SHEET 3 A 4 TYR A 13 MET A 22 1 O GLY A 18 N PHE A 108 SHEET 4 A 4 GLN A 44 GLY A 45 -1 O GLY A 45 N VAL A 17 SHEET 1 B 5 ALA A 70 GLU A 75 0 SHEET 2 B 5 PHE A 108 PHE A 112 -1 N LEU A 109 O ALA A 74 SHEET 3 B 5 TYR A 13 MET A 22 1 O GLY A 18 N PHE A 108 SHEET 4 B 5 GLY A 102 GLN A 105 1 O GLY A 102 N ARG A 14 SHEET 5 B 5 LEU A 80 ASP A 83 -1 N LEU A 80 O GLN A 105 SHEET 1 C 3 TRP A 40 GLN A 41 0 SHEET 2 C 3 ILE A 28 ARG A 33 -1 N ALA A 31 O GLN A 41 SHEET 3 C 3 PHE A 131 VAL A 137 -1 N GLY A 132 O SER A 32 SITE 1 AC1 13 ASN A 16 ARG A 33 GLN A 41 GLN A 44 SITE 2 AC1 13 TYR A 82 PHE A 84 VAL A 88 LYS A 91 SITE 3 AC1 13 TRP A 96 GLN A 103 VAL A 147 PHE A 149 SITE 4 AC1 13 LYS A 150 CRYST1 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