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- PDB-7cuf: Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the... -

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Basic information

Entry
Database: PDB / ID: 7cuf
TitleCrystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.44 A resolution
ComponentsUric acid degradation bifunctional protein
KeywordsOXIDOREDUCTASE / catalytic mechanism / water structure / enzyme kinetics / enzyme structure / conformational flexibility / quasi-stable water molecule
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 / 2-METHOXYETHANOL / OXYGEN MOLECULE / Uric acid degradation bifunctional protein
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsHibi, T. / Itoh, T.
Citation
Journal: J.Biochem. / Year: 2021
Title: Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity.
Authors: Hibi, T. / Itoh, T.
#1: 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.
#2: 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.
History
DepositionAug 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 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)72,61515
Polymers71,6472
Non-polymers96913
Water12,574698
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)145,23130
Polymers143,2934
Non-polymers1,93826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area28440 Å2
ΔGint-81 kcal/mol
Surface area42230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.622, 133.850, 145.391
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 , 6 types, 711 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MXE / 2-METHOXYETHANOL / 2-Methoxyethanol


Mass: 76.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 50.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 16%(w/v) PEG 8000, 0.1M Tris/H2SO4, pH 8.3, 0.09 M K2SO4, 2mM 8-azaxanthine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 120337 / % possible obs: 97.9 % / Redundancy: 16.4 % / Biso Wilson estimate: 18.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.085 / Net I/σ(I): 13.6
Reflection shellResolution: 1.46→1.47 Å / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2 / Num. unique obs: 3561 / CC1/2: 0.845 / Rrim(I) all: 0.574 / % possible all: 92.4

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Processing

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

3wlv


Resolution: 1.46→40.14 Å / SU ML: 0.2035 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 6017 5 %
Rwork0.1992 114309 -
obs0.2007 120326 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.15 Å2
Refinement stepCycle: LAST / Resolution: 1.46→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 63 698 5560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00965051
X-RAY DIFFRACTIONf_angle_d1.09376853
X-RAY DIFFRACTIONf_chiral_restr0.0841760
X-RAY DIFFRACTIONf_plane_restr0.0081873
X-RAY DIFFRACTIONf_dihedral_angle_d6.4794683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.470.33571780.31753383X-RAY DIFFRACTION87.9
1.47-1.490.34371920.31233642X-RAY DIFFRACTION94.92
1.49-1.510.32351900.30153625X-RAY DIFFRACTION95.35
1.51-1.530.2961950.27943696X-RAY DIFFRACTION95.44
1.53-1.550.30771950.27173706X-RAY DIFFRACTION96.61
1.55-1.570.28181940.2723681X-RAY DIFFRACTION95.96
1.57-1.590.30261930.27183672X-RAY DIFFRACTION96.58
1.59-1.610.31051970.27323745X-RAY DIFFRACTION97.38
1.61-1.640.25981990.26443771X-RAY DIFFRACTION97.88
1.64-1.670.3261990.27673783X-RAY DIFFRACTION98.56
1.67-1.690.27792010.25713817X-RAY DIFFRACTION99.41
1.69-1.730.28892000.25953808X-RAY DIFFRACTION99.58
1.73-1.760.28282020.24823841X-RAY DIFFRACTION99.8
1.76-1.790.28192020.24473838X-RAY DIFFRACTION99.85
1.79-1.830.27572020.25353828X-RAY DIFFRACTION99.98
1.83-1.880.29462040.24453881X-RAY DIFFRACTION100
1.88-1.920.2772020.23833836X-RAY DIFFRACTION100
1.92-1.970.25552030.22573849X-RAY DIFFRACTION100
1.97-2.030.2522020.22553849X-RAY DIFFRACTION100
2.03-2.10.24892040.21613869X-RAY DIFFRACTION100
2.1-2.170.23012040.20813874X-RAY DIFFRACTION100
2.17-2.260.21992020.19693852X-RAY DIFFRACTION100
2.26-2.360.25372040.19523861X-RAY DIFFRACTION100
2.36-2.490.22992060.19723912X-RAY DIFFRACTION100
2.49-2.640.242030.1923874X-RAY DIFFRACTION100
2.64-2.850.23062070.18723921X-RAY DIFFRACTION100
2.85-3.130.20392040.18283883X-RAY DIFFRACTION100
3.13-3.590.19412070.16153939X-RAY DIFFRACTION100
3.59-4.520.17992090.14133966X-RAY DIFFRACTION99.98
4.52-40.140.18152170.16634107X-RAY DIFFRACTION99.93
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)
10.417909045161-0.253676668811-0.1547905537620.65806178809-0.06302022555130.8664941583460.1462560672730.110527251439-0.105097283365-0.150816912908-0.09155058599830.09869992100610.0841616573576-0.109240524792-0.05169293419150.2227283959540.00676341900934-0.05484043209510.147912419893-0.03168129512120.173969505525-11.1725165264-18.9991422608-43.5530751924
20.986994589915-0.210354907176-0.06865087988491.35511828983-0.6396271587081.597457983230.1265433759240.101333257679-0.17335952856-0.131987134241-0.09034667262290.1109793470130.16456339472-0.0623095268955-0.04705912651470.2426355582950.00217521682207-0.06484630980580.131721136289-0.02988094334020.202371822622-12.588608012-24.4805387369-43.4544278251
30.578131680446-0.3021183005-0.02572775633620.6624562234420.1947036998380.5204735401480.1080998756280.135908236097-0.0490450489691-0.0873229519172-0.05079148552650.03741233144750.103214430892-0.0462021305973-0.05858494574820.2029826461610.0346265257215-0.02622625611340.1543340040220.002160509343940.128404492036-10.1413052054-4.18091780092-50.5104127046
40.455546139886-0.07945241813890.1067498009511.948606557540.6946971794781.300036002720.1251672827720.126568241715-0.0316229531064-0.220981154434-0.1183266478550.06900843185760.0183919879411-0.109405363012-0.008252736292130.2021053427740.0708730705495-0.01076718551220.221891937915-0.002902274199260.169882667878-19.36847283242.02253177313-53.6193793264
52.245798868750.6437842271230.4398981813341.474138754490.4761124350771.341937807050.04084371085610.1394227574940.114615905841-0.261069647461-0.0644284231333-0.0626265518502-0.2185049015710.05004518768820.02386404398450.2132162540460.07266263767390.02195835306030.1486434320810.01674926396790.147097993713-10.711820779615.9956581014-45.5619140231
60.523578147273-0.2944220375570.4268770430860.223712181762-0.3751270625231.246784663450.0111273464478-0.07443209824740.00330249276221-0.002582990313880.0139687209973-0.0292251221123-0.0646950200798-0.118603837056-0.008992591104360.1368413188580.00338058930186-0.003721676398210.156556159161-0.0044742865810.131220309056-15.88645477126.98916064025-16.0295552438
71.05488939731-0.02215293805370.9447186768360.663085372213-0.07020237612262.07431916407-0.01667541821070.0134303328610.0276641411416-0.0781998847068-0.03889198755620.0474103542431-0.014776511629-0.196464682438-0.01990898333990.1533571687840.0405613943080.003649412490510.1695784210180.002576028601430.150127302113-25.618912648912.2574477182-38.0674642034
80.954906945702-0.4555423102660.5637834467971.23869277193-0.5066120555992.185991228240.0254103422506-0.05206972073970.01618516372570.061703449094-0.00106683455170.0547321595703-0.0795275835945-0.128946063348-0.03003234291980.0818498850950.007953327653560.01204612250150.12594027760.004379051456490.122304047064-24.125706092613.2117237305-25.5652510849
92.005885155210.3153691301541.771847287740.9155553925080.3695759655962.678331952240.0468158263453-0.26340273225-0.001863876756770.3233832979240.018798330221-0.127771682576-0.082026035045-0.00312059210152-0.01857087467460.248824720703-0.0100836303871-0.04365191175560.2091260531220.003108105222010.1839603212351.7224702903710.102130972-6.91852720581
100.152795133251-0.155994892544-0.05045094581350.497009619946-0.1201909302810.3000233413050.0382600377836-0.0125446042367-0.0842148531127-0.0124518388962-0.01283697160470.05206709060940.0598472859703-0.059158759007-0.02255061006650.122648072863-0.00643661651447-0.01095206659960.1308952873460.0003125161039590.146168043316-14.5554868981-5.34139258023-22.2334102715
110.834927297551-0.425104242567-0.18413171171.266351634330.6216066698191.415320639360.0321048060573-0.0819448926301-0.0791085539260.03346362730210.02297708995240.03767006190610.0991945896618-0.0786611302677-0.04638975720390.112183128689-0.0267977392632-0.006854960024880.1391374178080.03608541686470.142082533606-14.822413962-12.4590700619-15.5272884837
121.977294556271.17255136987-0.03413560127711.49784365720.5909429840323.29112145314-0.00842283228065-0.468160601395-0.4181431789810.2493882293670.100763369993-0.2802491695040.534823159770.522094016437-0.03354554577430.265653139470.0552021721035-0.02916629516630.320272359690.03378975649280.2620031049489.77128088436-22.1039414627-20.1712477517
131.743949913740.201410566814-0.8252925825590.5500774000130.07198441929241.244927951-0.03799435409810.1037820668140.05764827601710.02954707429260.02017630832990.04343666124210.153769921895-0.1317230880570.03805045245110.168695400516-0.0223136130756-0.01670799433910.119573115685-0.004395378455760.151238231199-7.26067685526-17.0718057527-26.1210674362
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 72 )AA8 - 721 - 65
22chain 'A' and (resid 73 through 119 )AA73 - 11966 - 112
33chain 'A' and (resid 120 through 192 )AA120 - 192113 - 186
44chain 'A' and (resid 193 through 276 )AA193 - 276187 - 271
55chain 'A' and (resid 277 through 310 )AA277 - 310272 - 305
66chain 'B' and (resid 8 through 43 )BJ8 - 431 - 36
77chain 'B' and (resid 44 through 72 )BJ44 - 7237 - 65
88chain 'B' and (resid 73 through 119 )BJ73 - 11966 - 113
99chain 'B' and (resid 120 through 135 )BJ120 - 135114 - 129
1010chain 'B' and (resid 136 through 192 )BJ136 - 192130 - 189
1111chain 'B' and (resid 193 through 276 )BJ193 - 276190 - 275
1212chain 'B' and (resid 277 through 292 )BJ277 - 292276 - 291
1313chain 'B' and (resid 293 through 310 )BJ293 - 310292 - 309

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