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- PDB-4r99: Crystal structure of a uricase from Bacillus fastidious -

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Basic information

Entry
Database: PDB / ID: 4r99
TitleCrystal structure of a uricase from Bacillus fastidious
ComponentsUricase
KeywordsHYDROLASE / Bacillus fastidious uricase / fold / stability
Function / homology
Function and homology information


purine nucleobase catabolic process / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / peroxisome
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
factor independent urate hydroxylase
Similarity search - Component
Biological speciesBacillus fastidiosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFeng, J. / Wang, L. / Liu, H.B. / Liu, L. / Liao, F.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Crystal structure of Bacillus fastidious uricase reveals an unexpected folding of the C-terminus residues crucial for thermostability under physiological conditions.
Authors: Feng, J. / Wang, L. / Liu, H. / Yang, X. / Liu, L. / Xie, Y. / Liu, M. / Zhao, Y. / Li, X. / Wang, D. / Zhan, C.G. / Liao, F.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,12310
Polymers149,5464
Non-polymers5766
Water25,5811420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24000 Å2
ΔGint-199 kcal/mol
Surface area47550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.195, 77.415, 77.777
Angle α, β, γ (deg.)111.22, 90.55, 114.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uricase


Mass: 37386.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus fastidiosus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: C5HDG5, 3-hydroxyisobutyryl-CoA hydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1420 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl, 0.2M ammonium sulfate, 25%(w/v) PEG-3350 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 128276 / Num. obs: 122119 / % possible obs: 95.2 %
Reflection shellResolution: 1.8→1.86 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R8X

4r8x


Resolution: 1.8→40.288 Å / FOM work R set: 0.8135 / SU ML: 0.23 / σ(F): 1.96 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 6067 5.03 %
Rwork0.228 114456 -
obs0.2293 120523 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.27 Å2 / Biso mean: 26.18 Å2 / Biso min: 12.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9930 0 30 1420 11380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310201
X-RAY DIFFRACTIONf_angle_d0.9113867
X-RAY DIFFRACTIONf_chiral_restr0.0631545
X-RAY DIFFRACTIONf_plane_restr0.0031813
X-RAY DIFFRACTIONf_dihedral_angle_d11.9033573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.2822010.27253893409496
1.8205-1.84190.29872350.26493823405895
1.8419-1.86440.34882130.28793918413196
1.8644-1.8880.31732120.28843827403996
1.888-1.91280.57761780.51543439361785
1.9128-1.9390.64241370.56742909304671
1.939-1.96670.35371890.30783829401896
1.9667-1.99610.2642100.2493942415296
1.9961-2.02720.27441950.24523872406796
2.0272-2.06050.28722010.30673843404495
2.0605-2.0960.35611860.30043767395392
2.096-2.13410.30212040.25793845404996
2.1341-2.17520.2842080.23243868407696
2.1752-2.21960.28442260.24213908413496
2.2196-2.26780.49422020.44823521372388
2.2678-2.32060.26351700.26033892406296
2.3206-2.37860.2831890.22763965415497
2.3786-2.44290.24582040.23053935413997
2.4429-2.51480.23932130.22453927414097
2.5148-2.59590.24922170.22043922413997
2.5959-2.68870.2632180.21723888410697
2.6887-2.79630.23441960.21863935413197
2.7963-2.92350.22172190.21063930414997
2.9235-3.07760.23442100.20133948415897
3.0776-3.27040.19382340.18983901413597
3.2704-3.52270.2022070.18063945415297
3.5227-3.8770.23411830.18813480366386
3.877-4.43740.17031870.16873689387691
4.4374-5.58830.17242050.15853998420398
5.5883-40.29830.1972180.18373897411597
Refinement TLS params.Method: refined / Origin x: -9.2295 Å / Origin y: -36.1606 Å / Origin z: 14.8884 Å
111213212223313233
T0.1191 Å2-0.0099 Å20.0099 Å2-0.1071 Å2-0.0024 Å2--0.111 Å2
L0.2952 °2-0.0314 °20.0202 °2-0.2612 °20.0492 °2--0.4936 °2
S0.0044 Å °-0.0103 Å °0.0103 Å °0.0094 Å °0.0036 Å °-0.0076 Å °-0.014 Å °0.0304 Å °-0.0085 Å °
Refinement TLS groupSelection details: ALL

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