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- PDB-1gth: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1gth
TitleDIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL
ComponentsDIHYDROPYRIMIDINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 5-FLUOROURACIL DEGRADATION
Function / homology
Function and homology information


dihydropyrimidine dehydrogenase (NADP+) / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / uracil binding / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / flavin adenine dinucleotide binding / NADP binding ...dihydropyrimidine dehydrogenase (NADP+) / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / uracil binding / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / flavin adenine dinucleotide binding / NADP binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain ...Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / (5S)-5-IODODIHYDRO-2,4(1H,3H)-PYRIMIDINEDIONE / 5-IODOURACIL / Chem-NDP / IRON/SULFUR CLUSTER / URACIL / Dihydropyrimidine dehydrogenase [NADP(+)]
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y.
Citation
Journal: J. Biol. Chem. / Year: 2002
Title: Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
Authors: Dobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Study of Pig Liver Dihydropyrimidine Dehydrogenase
Authors: Dobritzsch, D. / Persson, K. / Schneider, G. / Lindqvist, Y.
History
DepositionJan 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection / Category: atom_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL, THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPYRIMIDINE DEHYDROGENASE
B: DIHYDROPYRIMIDINE DEHYDROGENASE
C: DIHYDROPYRIMIDINE DEHYDROGENASE
D: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,81936
Polymers446,4134
Non-polymers14,40632
Water55,3603073
1
A: DIHYDROPYRIMIDINE DEHYDROGENASE
B: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,47418
Polymers223,2072
Non-polymers7,26816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DIHYDROPYRIMIDINE DEHYDROGENASE
D: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,34518
Polymers223,2072
Non-polymers7,13816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.210, 159.690, 167.590
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.0015, -0.004), (0.0019, -0.6979, -0.7162), (-0.0039, -0.7162, 0.6979)116.7223, 176.72121, 74.8225
2given(1, 0.0036, 0.0009), (-0.0023, 0.7927, -0.6096), (-0.003, 0.6096, 0.7927)-13.5323, 12.9793, -28.6192
3given(-1, -0.0036, -0.0049), (0.0043, -0.989, -0.148), (-0.0043, -0.148, 0.989)102.6084, 199.3446, -76.4262

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DIHYDROPYRIMIDINE DEHYDROGENASE / / DPD / DHPDHASE / DIHYDROURACIL DEHYDROGENASE / DIHYDROTHYMINE DEHYDROGENASE


Mass: 111603.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Organ: LIVER / Plasmid: PSE420 / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+)

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Non-polymers , 8 types, 3105 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical ChemComp-IDH / (5S)-5-IODODIHYDRO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 239.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5IN2O2
#7: Chemical ChemComp-IUR / 5-IODOURACIL


Mass: 237.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3IN2O2
#8: Chemical ChemComp-URA / URACIL / Uracil


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3073 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 671 IS S-(HEXAHYDRO-2,4-DIOXO-5-PYRIMIDINYL) CYSTEINE, WHICH ORIGINATES FROM ALKYLATION OF ...RESIDUE 671 IS S-(HEXAHYDRO-2,4-DIOXO-5-PYRIMIDINYL) CYSTEINE, WHICH ORIGINATES FROM ALKYLATION OF CYSTEINE BY 5-IODO-5,6-DIHYDROURACIL

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.5
Details: 100 MM SODIUM CITRATE PH 4.7, 16-20 % POLYETHYLENE GLYCOL 6000, 1 MM DTT, 5 MM 5-IODOURACIL, 5 MM NADPH
Crystal grow
*PLUS
Temperature: 293 K / pH: 4.7 / Method: vapor diffusion / Details: Dobritzsch, D., (2001) Acta Crystallogr., 57, 153.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117-22 %(w/v)PEG60001reservoir
210 mMdithiothreitol1reservoir
3100 mMsodium citrate1reservoirpH4.7
44.5 mg/mlDPD1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9311
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9311 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 200114 / % possible obs: 98.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.3
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.2 / % possible all: 97.4
Reflection
*PLUS
Num. obs: 199249
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIHYDROPYRIMIDINE DEHYDROGENASE, UNCOMPLEXED

Resolution: 2.25→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3543123 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE 5 C-TERMINAL RESIDUES AND A FEW LOOP-RESIDUES WERE NOT SEEN IN THE DENSITY DUE TO DISORDER
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3984 2 %RANDOM
Rwork0.177 ---
obs0.177 199143 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.445 Å2 / ksol: 0.342276 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.16 Å20 Å20.91 Å2
2--9.51 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30999 0 690 3073 34762
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.35 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.244 478 2 %
Rwork0.215 24026 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PG2.PARWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAMPG2.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMNEWSUB.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.11
LS refinement shell
*PLUS
Rfactor obs: 0.215

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