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- PDB-4h00: The crystal structure of mon-Zn dihydropyrimidinase from Tetraodo... -

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Basic information

Entry
Database: PDB / ID: 4h00
TitleThe crystal structure of mon-Zn dihydropyrimidinase from Tetraodon nigroviridis
Componentsdihydropyrimidinase
KeywordsHYDROLASE / carboxylation / zinc binding / Alpha-Beta Barrel
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm
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
Biological speciesTetraodon nigroviridis (spotted green pufferfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHsieh, 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 Structural Requirements for Post-translational Modification
Authors: Hsieh, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9962
Polymers56,9301
Non-polymers651
Water3,711206
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)113,9924
Polymers113,8612
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area3220 Å2
ΔGint-93 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.998, 160.998, 94.370
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-796-

HOH

21A-822-

HOH

31A-832-

HOH

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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)
Gene: DPYS / Plasmid: pET44a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: H3C542*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: lithium sulfate monohydrate, PEG 4000 (12%, w/v), tris-sodium citrate dihydrate (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-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionResolution: 2→30 Å / Num. all: 40712 / Num. obs: 40386 / % possible obs: 99.2 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Rsym value: 0.042
Reflection shellResolution: 2→2.03 Å / % possible all: 99.6

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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: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.229 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20427 2100 5 %RANDOM
Rwork0.17049 ---
obs0.17219 39533 99.16 %-
all-39867 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.872 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20 Å2
2---1.35 Å20 Å2
3---2.7 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 1 206 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193842
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9485202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5075484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69423.526173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43115643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2821529
X-RAY DIFFRACTIONr_chiral_restr0.1450.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212933
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
Rfree0.27 151 -
Rwork0.232 2719 -
obs--99.62 %

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