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- PDB-4lcq: The crystal structure of di-Zn dihydropyrimidinase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4lcq
TitleThe crystal structure of di-Zn dihydropyrimidinase in complex with NCBI
Componentsdihydropyrimidinase
KeywordsHYDROLASE ACTIVATOR / Hydrolase / Zinc binding / carboxylation / Alpha-Beta Barrel
Function / homology
Function and homology information


pyrimidine nucleobase catabolic process / dihydropyrimidinase activity / metal ion binding / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(2S)-3-(carbamoylamino)-2-methylpropanoic acid / Dihydropyrimidinase
Similarity search - Component
Biological speciesTetraodon nigroviridis (spotted green pufferfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsHsieh, Y.C. / Chen, M.C. / Hsu, C.C. / Chan, S.I. / Yang, Y.S. / Chen, C.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal structures of vertebrate dihydropyrimidinase and complexes from Tetraodon nigroviridis with lysine carbamylation: metal and structural requirements for post-translational modification and function.
Authors: Hsieh, Y.C. / Chen, M.C. / Hsu, C.C. / Chan, S.I. / Yang, Y.S. / Chen, C.J.
History
DepositionJun 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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_comp_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.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2074
Polymers56,9301
Non-polymers2773
Water4,450247
1
A: dihydropyrimidinase
hetero molecules

A: dihydropyrimidinase
hetero molecules

A: dihydropyrimidinase
hetero molecules

A: dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,82916
Polymers227,7214
Non-polymers1,10812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area11140 Å2
ΔGint-37 kcal/mol
Surface area60840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.204, 161.204, 93.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein dihydropyrimidinase


Mass: 56930.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetraodon nigroviridis (spotted green pufferfish)
Plasmid: pET44a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4SMR4*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-URQ / (2S)-3-(carbamoylamino)-2-methylpropanoic acid


Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE FIRST 20 RESIDUES ARE EXPRESSION TAGS.

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: lithium sulfate monohydrate (100mM), PEG 4000 (12%, w/v), tris-sodium citrate dihydrate (100mM, pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONNSRRC BL13B11
SYNCHROTRONSPring-8 BL12B22
Detector
TypeIDDetector
ADSC QUANTUM 4r1CCD
ADSC QUANTUM 315r2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 110112 / Num. obs: 109892 / % possible obs: 99.8 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 4.4
Reflection shellResolution: 1.8→1.86 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.193 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 1.81 / ESU R: 0.105 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20048 2871 5.1 %RANDOM
Rwork0.17383 ---
obs0.17524 53624 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.341 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2---1.15 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 12 247 4018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.9495211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41223.526173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95115643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3171529
X-RAY DIFFRACTIONr_chiral_restr0.1770.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0320.0212939
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 191 -
Rwork0.227 3716 -
obs--100 %

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