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- PDB-1h7x: Dihydropyrimidine dehydrogenase (DPD) from pig, ternary complex o... -

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Basic information

Entry
Database: PDB / ID: 1h7x
TitleDihydropyrimidine dehydrogenase (DPD) from pig, ternary complex of a mutant enzyme (C671A), NADPH and 5-fluorouracil
ComponentsDIHYDROPYRIMIDINE DEHYDROGENASE
KeywordsELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 5-FLUOROURACIL DEGRADATION / OXIDOREDUCTASE
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 / NADP binding / flavin adenine dinucleotide 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 / NADP binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol
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 / FAD/NAD(P)-binding domain / 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 / 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 / Chem-NDP / IRON/SULFUR CLUSTER / 5-FLUOROURACIL / Dihydropyrimidine dehydrogenase [NADP(+)]
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsDobritzsch, D. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y.
Citation
Journal: Embo J. / Year: 2001
Title: Crystal Structure of Dihydropyrimidine Dehydrogenase, a Major Determinant of the Pharmacokinetics of the Anti-Cancer Drug 5-Fluorouracil
Authors: Dobritzsch, D. / 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 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 17, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / diffrn_source / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.value
Revision 2.1Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _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 2.2May 1, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF, BF, CF, DF" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF, BF, CF, DF" IN EACH CHAIN ON SHEET RECORDS ARE 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)460,38136
Polymers446,2854
Non-polymers14,09632
Water77,2664289
1
A: DIHYDROPYRIMIDINE DEHYDROGENASE
B: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,19018
Polymers223,1432
Non-polymers7,04816
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)230,19018
Polymers223,1432
Non-polymers7,04816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.950, 159.290, 163.570
Angle α, β, γ (deg.)90.00, 96.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999998, 0.001778, -0.00041), (-0.001716, -0.840285, 0.542142), (0.000619, 0.542142, 0.840287)155.12051, 62.97818, -18.55704
2given(-0.999998, -0.001657, 0.001065), (-0.001964, 0.796369, -0.604807), (0.000154, -0.604808, -0.796371)129.92288, 87.18368, 96.23115
3given(0.999982, 0.005489, -0.002623), (0.005659, -0.99752, 0.070158), (-0.002231, -0.070172, -0.997532)-25.44943, 147.75595, 73.56749

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 111571.281 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Cellular location: CYTOPLASM / Gene: DPYD / Plasmid: PSE420 / Gene (production host): DPYD / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+)

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Non-polymers , 6 types, 4321 molecules

#2: Chemical
ChemComp-SF4 / 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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-FAD / 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


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical
ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4289 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN A, B, C, D ENGINEERED MUTATION CYS671ALA INVOLVED IN THE CATABOLISM OF URACIL AND THYMIDINE ...CHAIN A, B, C, D ENGINEERED MUTATION CYS671ALA INVOLVED IN THE CATABOLISM OF URACIL AND THYMIDINE LEADING TO THE FORMATION OF BETA-ALANINE. CATALYSES THE REDUCTION OF URACIL AND THYMINE.

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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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.7
Details: 100 MM SODIUM CITRATE PH 4.7, 16-20 % POLYETHYLENE GLYCOL 6000, 1 MM DTT, 1 MM NADPH, 5 MM 5FU
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119-22 %(w/v)PEG60001reservoir
2100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9746
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9746 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 274925 / % possible obs: 99 % / Redundancy: 2.8 % / Biso Wilson estimate: 8.7 Å2 / Rsym value: 0.063 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.166 / % possible all: 95.8
Reflection
*PLUS
Num. measured all: 1471519 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 95.8 % / Rmerge(I) obs: 0.166

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Processing

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

Resolution: 2.01→25.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4072791.96 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUES WERE NOT SEEN IN THE DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.192 5418 2 %RANDOM
Rwork0.171 ---
obs0.171 273624 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48 Å2 / ksol: 0.371281 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å2-1.99 Å2
2--3.77 Å20 Å2
3----1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.01→25.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31056 0 692 4289 36037
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_deg1.5
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_d3.13
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
Refine LS restraints NCSRms dev Biso : 2 Å2 / Rms dev position: 0.16 Å
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.229 574 2 %
Rwork0.193 28847 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PG2.PARWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE_FU.PARAMPG2.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMSUBS.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.13

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