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- PDB-4r8x: Crystal structure of a uricase from Bacillus fastidious -

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Basic information

Entry
Database: PDB / ID: 4r8x
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: 1.401 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
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
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
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


Theoretical massNumber of molelcules
Total (without water)143,4394
Polymers143,4394
Non-polymers00
Water34,5171916
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22560 Å2
ΔGint-103 kcal/mol
Surface area47360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.152, 77.473, 77.295
Angle α, β, γ (deg.)68.65, 65.01, 90.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uricase


Mass: 35859.809 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1916 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris, 20% PEG 3350, 0.2M sodium citrate, pH 8.5, 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: 1.4→50 Å / Num. all: 269102 / Num. obs: 256186 / % possible obs: 95.2 % / Biso Wilson estimate: 14.12 Å2
Reflection shellResolution: 1.4→1.45 Å / % possible all: 93.1

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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: 1J2G

1j2g


Resolution: 1.401→32.039 Å / FOM work R set: 0.8645 / SU ML: 0.15 / σ(F): 1.96 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 12864 5.02 %Random
Rwork0.1722 ---
all0.1739 269102 --
obs0.1739 256138 95.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.08 Å2 / Biso mean: 19.22 Å2 / Biso min: 9.18 Å2
Refinement stepCycle: LAST / Resolution: 1.401→32.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9905 0 0 1916 11821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610190
X-RAY DIFFRACTIONf_angle_d1.08113842
X-RAY DIFFRACTIONf_chiral_restr0.0751543
X-RAY DIFFRACTIONf_plane_restr0.0051811
X-RAY DIFFRACTIONf_dihedral_angle_d12.5713642
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 (%)
1.4005-1.41640.28354430.22437663810690
1.4164-1.43310.25724030.20847962836593
1.4331-1.45060.26194360.20297932836893
1.4506-1.46890.25054190.19777908832793
1.4689-1.48820.26394550.19348018847393
1.4882-1.50860.24434130.19278002841594
1.5086-1.53020.25364200.17987905832594
1.5302-1.5530.21544580.16538011846994
1.553-1.57730.22944330.16288004843794
1.5773-1.60320.22124090.16277988839794
1.6032-1.63080.22664020.16088096849894
1.6308-1.66040.20354160.15868053846994
1.6604-1.69240.23524460.16728097854395
1.6924-1.72690.23094240.16228066849095
1.7269-1.76450.21343970.15928124852195
1.7645-1.80550.21284080.16138165857395
1.8055-1.85070.22794390.16348122856195
1.8507-1.90070.20714280.16038185861396
1.9007-1.95660.20583860.168167855396
1.9566-2.01980.20314350.16248220865596
2.0198-2.09190.19624280.15868267869596
2.0919-2.17570.20484320.16528136856896
2.1757-2.27470.19884380.1698306874497
2.2747-2.39460.21824400.18238168860897
2.3946-2.54450.22814640.19128252871697
2.5445-2.74090.22954660.19888256872297
2.7409-3.01650.20714240.18598271869597
3.0165-3.45260.18994170.17318272868997
3.4526-4.34820.17374310.15398437886899
4.3482-32.04760.17634540.17148221867596

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