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- PDB-4gz7: The crystal structure of Apo-dihydropyrimidinase from Tetraodon n... -

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Basic information

Entry
Database: PDB / ID: 4gz7
TitleThe crystal structure of Apo-dihydropyrimidinase from Tetraodon nigroviridis
Componentsdihydropyrimidinase
KeywordsHYDROLASE / carboxylation / zinc binding / 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
(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Dihydropyrimidinase
Similarity search - Component
Biological speciesTetraodon nigroviridis (spotted green pufferfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHsien, Y.C. / Chen, M.C. / Hsu, C.C. / Chan, S.I. / Yang, Y.S. / Chen, C.J.
CitationJournal: To be Published
Title: Lysine Carboxylation: Metal and Structure Requirements for Post-translational Modification
Authors: Hsien, Y.C. / Chen, M.C. / Hsu, C.C. / Chan, S.I. / Yang, Y.S. / Chen, C.J.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)55,6244
Polymers55,0541
Non-polymers5703
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: dihydropyrimidinase
hetero molecules

A: dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2488
Polymers110,1072
Non-polymers1,1416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area7040 Å2
ΔGint-26 kcal/mol
Surface area33230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.823, 160.823, 94.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-916-

HOH

21A-917-

HOH

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Components

#1: Protein dihydropyrimidinase


Mass: 55053.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetraodon nigroviridis (spotted green pufferfish)
Gene: DPYS / Plasmid: pET44a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: H3C542*PLUS
#2: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M lithium sulfate monohydrat, PEG 4000 12% w/v, iso-propanol 2% v/v, n-(2-acetamido)-iminodiacetic acid (ADA) buffer, 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 3152CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→44886 Å / Num. all: 44645 / Num. obs: 44645 / % possible obs: 99.3 % / Observed criterion σ(F): 11.8 / Observed criterion σ(I): 11.8 / Redundancy: 9.7 % / Rsym value: 0.045 / Net I/σ(I): 25.6
Reflection shellResolution: 1.95→2.1 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 11.8 / Num. unique all: 8846 / Rsym value: 0.41 / % 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: 2→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.678 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19472 2094 5 %RANDOM
Rwork0.1588 ---
obs0.1606 39580 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.363 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---1 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 39 232 4076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193924
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9525310
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96723.543175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67915652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4441529
X-RAY DIFFRACTIONr_chiral_restr0.1640.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213000
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 161 -
Rwork0.15 2713 -
obs--100 %

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