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

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Basic information

Entry
Database: PDB / ID: 7cmq
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 / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / allantoin metabolic process / purine nucleobase metabolic process
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: 1.65 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: 5Z2A
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

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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)72,42312
Polymers71,6472
Non-polymers77710
Water6,954386
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)144,84624
Polymers143,2934
Non-polymers1,55320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area27040 Å2
ΔGint-69 kcal/mol
Surface area42310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.063, 133.443, 144.514
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, factor-independent urate hydroxylase

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Non-polymers , 5 types, 396 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 / Oxygen


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 / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.43 Å3/Da / Density % sol: 49.5 %
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: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→46.1 Å / Num. obs: 82336 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Net I/σ(I): 13.96
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 25541 / CC1/2: 0.723 / Rrim(I) all: 0.788 / % possible all: 98.8

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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: 1.65→46.1 Å / SU ML: 0.1717 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1974 4115 5 %
Rwork0.1687 78208 -
obs0.1701 82323 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.219 Å
Refinement stepCycle: LAST / Resolution: 1.65→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 51 386 5221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094997
X-RAY DIFFRACTIONf_angle_d1.03636780
X-RAY DIFFRACTIONf_chiral_restr0.0603756
X-RAY DIFFRACTIONf_plane_restr0.0071865
X-RAY DIFFRACTIONf_dihedral_angle_d14.34571782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.35241330.32932539X-RAY DIFFRACTION95.74
1.67-1.690.25251430.24812711X-RAY DIFFRACTION100
1.69-1.710.28721400.24532658X-RAY DIFFRACTION99.93
1.71-1.730.26831420.22762698X-RAY DIFFRACTION99.93
1.73-1.760.28221400.2112660X-RAY DIFFRACTION100
1.76-1.780.22561420.19952696X-RAY DIFFRACTION100
1.78-1.810.24121410.19772690X-RAY DIFFRACTION99.93
1.81-1.840.21141420.19072688X-RAY DIFFRACTION100
1.84-1.870.21491420.18982695X-RAY DIFFRACTION99.93
1.87-1.90.20861410.1862679X-RAY DIFFRACTION100
1.9-1.930.21521430.18642711X-RAY DIFFRACTION100
1.93-1.970.21251410.17262692X-RAY DIFFRACTION100
1.97-2.010.18571420.16832691X-RAY DIFFRACTION99.93
2.01-2.050.21271410.16262675X-RAY DIFFRACTION100
2.05-2.10.18161410.16162685X-RAY DIFFRACTION100
2.1-2.160.1781420.15642700X-RAY DIFFRACTION100
2.16-2.210.21311420.15482699X-RAY DIFFRACTION100
2.21-2.280.19871420.15822705X-RAY DIFFRACTION99.96
2.28-2.350.20311420.1622688X-RAY DIFFRACTION99.89
2.35-2.440.20821430.16742728X-RAY DIFFRACTION100
2.44-2.530.20451430.16872716X-RAY DIFFRACTION99.97
2.53-2.650.20761420.16012693X-RAY DIFFRACTION100
2.65-2.790.16751430.15882722X-RAY DIFFRACTION99.97
2.79-2.960.16671450.15922744X-RAY DIFFRACTION100
2.96-3.190.17261430.16212719X-RAY DIFFRACTION99.93
3.19-3.510.19491440.16432746X-RAY DIFFRACTION100
3.51-4.020.1781460.16012767X-RAY DIFFRACTION99.83
4.02-5.070.16981450.13922745X-RAY DIFFRACTION98.97
5.07-46.10.23581390.20132668X-RAY DIFFRACTION91.7
Refinement TLS params.Method: refined / Origin x: 13.9650704308 Å / Origin y: 4.19013357373 Å / Origin z: 38.4381304565 Å
111213212223313233
T0.149884094212 Å2-0.0074539576614 Å20.0168633028026 Å2-0.204934601146 Å20.0132161268101 Å2--0.180816179094 Å2
L0.646157778513 °2-0.0972624147032 °20.00867215418612 °2-0.512976112113 °2-0.00630034706704 °2--0.514566471471 °2
S0.0202111329873 Å °0.213547263374 Å °0.0776540787873 Å °-0.0664190433456 Å °0.00451789850427 Å °-0.0605469799486 Å °-0.0339719317936 Å °0.064762113194 Å °-0.0232136223697 Å °
Refinement TLS groupSelection details: all

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