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- PDB-7cmn: Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by... -

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Basic information

Entry
Database: PDB / ID: 7cmn
TitleCrystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 88% RH.
ComponentsUric acid degradation bifunctional protein
KeywordsOXIDOREDUCTASE / protein engineering / enzyme / loop flexibility / entropy of activation
Function / homology
Function and homology information


2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / factor-independent urate hydroxylase / urate oxidase activity / allantoin metabolic process / urate catabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily / OHCU decarboxylase / Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
8-AZAXANTHINE / OXYGEN MOLECULE / Uric acid degradation bifunctional protein
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsHibi, T. / Itoh, T. / Nishiya, Y.
Citation
Journal: To be published
Title: Flexibility of a Distal Interface Loop Modulates Water Network in the Active Site of Bacillus sp. TB-90 Urate Oxidase
Authors: Hibi, T. / Itoh, T. / Nishiya, Y.
#1: Journal: Biochemistry / Year: 2016
Title: Hyperstabilization of Tetrameric Bacillus sp. TB-90 Urate Oxidase by Introducing Disulfide Bonds through Structural Plasticity.
Authors: Hibi, T. / Kume, A. / Kawamura, A. / Itoh, T. / Fukada, H. / Nishiya, Y.
#2: Journal: Biochemistry / Year: 2014
Title: Intersubunit salt bridges with a sulfate anion control subunit dissociation and thermal stabilization of Bacillus sp. TB-90 urate oxidase.
Authors: Hibi, T. / Hayashi, Y. / Fukada, H. / Itoh, T. / Nago, T. / Nishiya, Y.
History
DepositionJul 28, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 12, 2020ID: 5Z29
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uric acid degradation bifunctional protein
B: Uric acid degradation bifunctional protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,48513
Polymers71,6472
Non-polymers83911
Water9,980554
1
A: Uric acid degradation bifunctional protein
B: Uric acid degradation bifunctional protein
hetero molecules

A: Uric acid degradation bifunctional protein
B: Uric acid degradation bifunctional protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,97126
Polymers143,2934
Non-polymers1,67722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area27320 Å2
ΔGint-67 kcal/mol
Surface area41610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.889, 132.912, 144.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uric acid degradation bifunctional protein / Urate oxidase


Mass: 35823.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (strain TB-90) (bacteria) / Strain: TB-90 / Gene: uao / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: Q45697, 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, factor-independent urate hydroxylase

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Non-polymers , 5 types, 565 molecules

#2: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 8000, 0.1 M Tris-HCl, 0.08 M K2SO4, 2 mM 8-azaxthantine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→47.23 Å / Num. obs: 127636 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.072 / Net I/σ(I): 11.67
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 39778 / CC1/2: 0.829 / Rrim(I) all: 0.502 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WLV

3wlv


Resolution: 1.42→47.23 Å / SU ML: 0.1959 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2227 6380 5 %
Rwork0.2 121205 -
obs0.2011 127585 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.76 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.42→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 55 554 5379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095005
X-RAY DIFFRACTIONf_angle_d0.87836791
X-RAY DIFFRACTIONf_chiral_restr0.0774757
X-RAY DIFFRACTIONf_plane_restr0.006862
X-RAY DIFFRACTIONf_dihedral_angle_d15.27581786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.430.40572000.36433806X-RAY DIFFRACTION95.15
1.43-1.450.31382120.30984033X-RAY DIFFRACTION100
1.45-1.470.37922120.30124016X-RAY DIFFRACTION100
1.47-1.490.30982130.30074049X-RAY DIFFRACTION99.95
1.49-1.510.31952130.29634045X-RAY DIFFRACTION99.93
1.51-1.530.31482100.2933987X-RAY DIFFRACTION99.98
1.53-1.550.29882120.28564027X-RAY DIFFRACTION100
1.55-1.570.30482120.27924024X-RAY DIFFRACTION100
1.57-1.60.28472120.27784031X-RAY DIFFRACTION100
1.6-1.620.33762130.27744056X-RAY DIFFRACTION99.95
1.62-1.650.29882130.27084033X-RAY DIFFRACTION99.98
1.65-1.680.27642130.26054055X-RAY DIFFRACTION99.98
1.68-1.710.26932110.25044013X-RAY DIFFRACTION100
1.71-1.750.25822120.25014024X-RAY DIFFRACTION100
1.75-1.790.2872140.24594056X-RAY DIFFRACTION99.98
1.79-1.830.28832140.244078X-RAY DIFFRACTION100
1.83-1.870.24672120.23344017X-RAY DIFFRACTION99.98
1.87-1.930.27912130.22394065X-RAY DIFFRACTION100
1.93-1.980.24012140.22044047X-RAY DIFFRACTION99.98
1.98-2.050.23272140.21124067X-RAY DIFFRACTION100
2.05-2.120.19982120.2074034X-RAY DIFFRACTION100
2.12-2.20.19642140.18774060X-RAY DIFFRACTION99.98
2.2-2.30.19932140.18334069X-RAY DIFFRACTION99.98
2.3-2.430.18872150.17744097X-RAY DIFFRACTION99.98
2.43-2.580.21632140.1854054X-RAY DIFFRACTION99.95
2.58-2.780.20712160.17284111X-RAY DIFFRACTION100
2.78-3.060.17212160.16714107X-RAY DIFFRACTION99.98
3.06-3.50.19592180.16344125X-RAY DIFFRACTION99.91
3.5-4.410.18242150.15564098X-RAY DIFFRACTION98.47
4.41-47.230.2032070.18313921X-RAY DIFFRACTION90.79
Refinement TLS params.Method: refined / Origin x: -14.1958172422 Å / Origin y: -4.11789301686 Å / Origin z: -33.7007861459 Å
111213212223313233
T0.130143973336 Å2-0.0419584725803 Å2-0.0129085410782 Å2-0.286963952626 Å2-0.0382959199871 Å2--0.10808021757 Å2
L1.20048344178 °2-0.0343028457802 °20.00213807846331 °2-0.498830209146 °28.95631633046E-5 °2--0.497737742605 °2
S-0.0466163578694 Å °0.499776034462 Å °-0.103821223738 Å °-0.0706965859753 Å °0.0477828305346 Å °0.0744074945383 Å °0.0116465874064 Å °-0.0524245445074 Å °0.00113941361793 Å °
Refinement TLS groupSelection details: all

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