PDB Short entry for 1F3Y HEADER HYDROLASE 06-JUN-00 1F3Y TITLE SOLUTION STRUCTURE OF THE NUDIX ENZYME DIADENOSINE TETRAPHOSPHATE TITLE 2 HYDROLASE FROM LUPINUS ANGUSTIFOLIUS L. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 35-199; COMPND 5 EC: 3.6.1.17; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-3 KEYWDS ENZYME, MIXED 4-STRANDED BETA SHEET, 2-STRANDED ANTIPARALLEL SHEET, KEYWDS 2 ALPHA-BETA-ALPHA SANDWICH, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR J.D.SWARBRICK,T.BASHTANNYK,D.MAKSEL,X.R.ZHANG,G.M.BLACKBURN, AUTHOR 2 K.R.GAYLER,P.R.GOOLEY REVDAT 4 10-NOV-21 1F3Y 1 REMARK SEQADV REVDAT 3 24-FEB-09 1F3Y 1 VERSN REVDAT 2 07-JAN-03 1F3Y 1 REMARK REVDAT 1 06-JUN-01 1F3Y 0 JRNL AUTH J.D.SWARBRICK,T.BASHTANNYK,D.MAKSEL,X.R.ZHANG,G.M.BLACKBURN, JRNL AUTH 2 K.R.GAYLER,P.R.GOOLEY JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE NUDIX ENZYME JRNL TITL 2 DIADENOSINE TETRAPHOSPHATE HYDROLASE FROM LUPINUS JRNL TITL 3 ANGUSTIFOLIUS L. JRNL REF J.MOL.BIOL. V. 302 1165 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11183782 JRNL DOI 10.1006/JMBI.2000.4085 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.7, DYANA 1.5,1.4, CNS 0.9 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), GUENTERT (DYANA), BRUNGER REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F3Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011213. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298 REMARK 210 PH : 6.5; 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 50MM; 50MM; 50MM; 40MM REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9MM U-15N, 13C; HYDROLASE 50MM REMARK 210 PHOSPHATE BUFFER, 1.5MM EDTA, REMARK 210 3MM DTT; 0.9MM U-15N,13C; REMARK 210 HYDROLASE 50MM PHOSPHATE BUFFER, REMARK 210 1.3MM EDTA, 1.5MM EDTA,3MM DTT; REMARK 210 1.2MM U-15N; HYDROLASE 50MM REMARK 210 PHOSPHATE BUFFER, 1.5MM EDTA, REMARK 210 3MM DTT; 1.2MM U-15N; HYDROLASE REMARK 210 20MM IMIDAZOLE BUFFER, 20MM MGCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : REMARK 210 CBCANH,CBCA(CO)NH,C(CO)NH_TOCSY,HNCO,(HCA)CO(CA)NH; HCACO,HCCH- REMARK 210 TOCSY,13C-NOESY-HSQC,(HB)CB(CGCD)HD,(HB)CB(CGCDCE)HE,HACAHB,13C_ REMARK 210 CT_HEQC,; HNHB,HNHA,15N-TOCSY-HSQC,15N-NOESY-HSQC,15N-IPAP-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 : XEASY 1.3.13, VNMR 6.1 B REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY,STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 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 ARG A 33 H ASP A 35 1.40 REMARK 500 H ILE A 28 O VAL A 137 1.46 REMARK 500 O ARG A 62 H GLY A 66 1.56 REMARK 500 O GLU A 71 H LYS A 111 1.58 REMARK 500 H SER A 32 O GLU A 133 1.59 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 5 -87.51 56.32 REMARK 500 1 MET A 6 127.39 64.59 REMARK 500 1 ARG A 15 106.44 -51.78 REMARK 500 1 ASN A 24 -5.74 -56.06 REMARK 500 1 LEU A 34 56.44 -55.49 REMARK 500 1 ASP A 35 -37.63 -177.35 REMARK 500 1 PRO A 43 152.73 -49.97 REMARK 500 1 GLN A 44 148.28 -177.80 REMARK 500 1 ASP A 48 -174.88 -69.17 REMARK 500 1 SER A 69 74.18 -61.55 REMARK 500 1 TRP A 79 -155.94 -92.62 REMARK 500 1 LEU A 80 105.31 -162.90 REMARK 500 1 PRO A 85 177.59 -57.94 REMARK 500 1 LEU A 92 -64.74 -120.29 REMARK 500 1 SER A 98 28.52 -171.85 REMARK 500 1 TRP A 100 -164.88 -67.14 REMARK 500 1 LYS A 101 0.90 165.45 REMARK 500 1 THR A 113 52.67 -98.39 REMARK 500 1 GLN A 117 -4.31 -56.70 REMARK 500 1 LEU A 121 26.82 42.91 REMARK 500 1 SER A 126 -13.93 80.86 REMARK 500 1 GLU A 127 -77.32 -91.51 REMARK 500 1 PRO A 129 -179.93 -65.87 REMARK 500 1 GLU A 130 -67.45 -95.06 REMARK 500 2 SER A 5 -98.13 70.08 REMARK 500 2 MET A 6 132.38 65.58 REMARK 500 2 ASN A 24 -5.63 -57.59 REMARK 500 2 GLN A 44 141.62 -170.57 REMARK 500 2 GLU A 49 -76.66 -46.92 REMARK 500 2 SER A 69 73.44 -62.41 REMARK 500 2 TYR A 82 37.07 -78.88 REMARK 500 2 ASP A 83 -110.03 25.30 REMARK 500 2 PHE A 84 -178.58 174.63 REMARK 500 2 PRO A 85 177.30 -55.21 REMARK 500 2 ARG A 89 -76.73 -58.84 REMARK 500 2 LEU A 92 -51.37 -121.88 REMARK 500 2 GLN A 95 -100.81 -79.16 REMARK 500 2 TRP A 96 29.84 40.90 REMARK 500 2 SER A 98 145.00 -175.38 REMARK 500 2 ASP A 99 84.40 58.15 REMARK 500 2 LYS A 101 6.83 167.51 REMARK 500 2 THR A 113 55.27 -95.77 REMARK 500 2 GLN A 117 -5.09 -57.65 REMARK 500 2 LEU A 121 -34.23 73.11 REMARK 500 2 GLU A 127 -47.98 -146.91 REMARK 500 2 GLU A 130 -72.77 -88.89 REMARK 500 2 PHE A 149 0.63 -57.07 REMARK 500 3 LEU A 3 120.91 63.52 REMARK 500 3 SER A 5 98.34 51.85 REMARK 500 3 TYR A 13 48.06 -98.55 REMARK 500 REMARK 500 THIS ENTRY HAS 652 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1F3Y A 1 165 UNP O04841 O04841_LUPAN 35 199 SEQADV 1F3Y GLY A 1 UNP O04841 TYR 35 ENGINEERED MUTATION SEQADV 1F3Y PRO A 2 UNP O04841 CYS 36 ENGINEERED MUTATION SEQADV 1F3Y LEU A 3 UNP O04841 HIS 37 ENGINEERED MUTATION SEQADV 1F3Y GLY A 4 UNP O04841 SER 38 ENGINEERED MUTATION 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 HELIX 1 1 ASP A 52 GLY A 66 1 15 HELIX 2 2 PRO A 85 LEU A 92 1 8 HELIX 3 3 ASN A 93 TRP A 96 5 4 HELIX 4 4 GLN A 115 ILE A 119 5 5 HELIX 5 5 THR A 138 THR A 146 1 9 HELIX 6 6 VAL A 147 PHE A 149 5 3 HELIX 7 7 LYS A 150 ALA A 162 1 13 HELIX 8 8 PRO A 163 LEU A 165 5 3 SHEET 1 A 4 GLN A 44 GLY A 46 0 SHEET 2 A 4 ASN A 16 MET A 22 -1 N VAL A 17 O GLY A 45 SHEET 3 A 4 GLN A 105 PHE A 112 1 O LYS A 106 N GLY A 18 SHEET 4 A 4 ALA A 70 GLU A 75 -1 O GLU A 71 N LYS A 111 SHEET 1 B 3 ILE A 36 GLN A 41 0 SHEET 2 B 3 ILE A 28 ARG A 33 -1 N ALA A 31 O GLN A 41 SHEET 3 B 3 PHE A 131 VAL A 137 -1 N GLY A 132 O SER A 32 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