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- PDB-5z2b: Crystal structure of highly active BTUO mutant P287G Improved by ... -

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Basic information

Entry
Database: PDB / ID: 5z2b
TitleCrystal structure of highly active BTUO mutant P287G Improved by Humidity Control at 86% 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 / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / 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 / Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase ...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 / Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
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: 1.901 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
DepositionJan 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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)74,72711
Polymers74,0392
Non-polymers6889
Water7,891438
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)149,45422
Polymers148,0784
Non-polymers1,37618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area25870 Å2
ΔGint-91 kcal/mol
Surface area40680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.351, 133.356, 145.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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: 37019.594 Da / Num. of mol.: 2 / Mutation: P287G
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 , 6 types, 447 molecules

#2: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3N5O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 47.85 %
Crystal growTemperature: 288 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
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: 1.9→50 Å / Num. obs: 50914 / % possible obs: 93.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.031 / Rrim(I) all: 0.076 / Net I/σ(I): 17.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2456 / CC1/2: 0.82 / Rpim(I) all: 0.324 / Rrim(I) all: 0.722 / Χ2: 0.991 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFP

4xfp


Resolution: 1.901→40.043 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.56
RfactorNum. reflection% reflection
Rfree0.2169 1859 3.94 %
Rwork0.1718 --
obs0.1736 47143 86.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.901→40.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 44 438 5159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074843
X-RAY DIFFRACTIONf_angle_d0.8026565
X-RAY DIFFRACTIONf_dihedral_angle_d9.4292828
X-RAY DIFFRACTIONf_chiral_restr0.051732
X-RAY DIFFRACTIONf_plane_restr0.006831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9009-1.95230.24941090.23932729X-RAY DIFFRACTION68
1.9523-2.00980.32951110.21683062X-RAY DIFFRACTION76
2.0098-2.07460.28261360.21553120X-RAY DIFFRACTION78
2.0746-2.14880.28271160.19453157X-RAY DIFFRACTION78
2.1488-2.23480.23461460.18963161X-RAY DIFFRACTION79
2.2348-2.33650.22541340.1793155X-RAY DIFFRACTION79
2.3365-2.45970.21641390.1813375X-RAY DIFFRACTION84
2.4597-2.61380.21971490.18183560X-RAY DIFFRACTION88
2.6138-2.81550.24521510.17863734X-RAY DIFFRACTION93
2.8155-3.09880.20941670.17273883X-RAY DIFFRACTION95
3.0988-3.54690.21851570.15814039X-RAY DIFFRACTION99
3.5469-4.46780.16881740.14234080X-RAY DIFFRACTION100
4.4678-40.05170.21211700.17024229X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21530.19330.14530.6605-0.10090.26760.15280.1814-0.0756-0.2717-0.05240.1726-0.0929-0.044-0.09980.31470.0677-0.06840.2456-0.05930.2304-9.013-14.8267-52.7983
20.2637-0.09010.0430.6210.04390.96580.08620.0414-0.1446-0.0845-0.07590.13570.1327-0.1069-0.01260.2597-0.0189-0.05730.1929-0.03660.2722-13.2221-24.3464-39.0619
31.77131.2017-3.1650.8391-1.88818.3077-0.13740.222-0.1519-0.3856-0.0459-0.06190.19130.42660.1180.420.07660.02670.3778-0.02120.26647.0444-6.7444-62.1323
40.6594-0.1983-0.03780.38240.12770.43260.11560.1668-0.0994-0.1067-0.04010.03310.0718-0.0946-0.06510.23710.0233-0.03440.2079-0.00170.1927-15.2052-3.2877-46.8531
50.4395-0.08550.00290.42420.60510.88590.12080.18880.0853-0.3126-0.04620.043-0.135-0.0187-0.03710.22890.0333-0.02350.27080.04530.2654-16.530910.113-47.4104
60.3738-0.1216-0.17391.42720.21220.39540.0630.2428-0.0872-0.1756-0.05880.17110.0646-0.13020.02020.32570.0533-0.06610.3133-0.0170.2297-19.7352-0.5818-57.2112
70.4046-0.3988-0.29620.52860.09550.71540.06920.051-0.0926-0.2595-0.11130.0516-0.1-0.18950.01230.25960.0283-0.01940.24510.01510.2255-15.92017.9701-46.0081
80.7275-0.22130.3870.3435-0.21950.83180.0404-0.00470.0765-0.026-0.00540.08150.0137-0.0982-0.02710.16140.0112-0.0010.18990.00530.2004-19.775210.9303-24.8386
90.7078-0.16390.18610.476-0.07720.53780.0107-0.00990.10490.1178-0.00610.0414-0.0108-0.0462-0.01990.18780.00280.0110.19240.01530.1999-16.748310.5948-19.6787
100.3196-0.09220.04670.16450.02290.4398-0.003-0.0451-0.0619-0.00220.03570.09040.0671-0.0844-0.02560.1659-0.0102-0.00850.1830.01740.206-14.5003-5.3453-22.2446
110.6073-0.1655-0.0590.69030.12360.95130.021-0.0565-0.129-0.00350.04010.09430.1322-0.0978-0.04350.1528-0.0273-0.01360.18560.0310.2177-12.0472-13.7762-17.7787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 263 )
7X-RAY DIFFRACTION7chain 'A' and (resid 264 through 310 )
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 91 )
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 135 )
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 192 )
11X-RAY DIFFRACTION11chain 'B' and (resid 193 through 310 )

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