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- PDB-7f2w: TbUox in complex with uric acid -

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Basic information

Entry
Database: PDB / ID: 7f2w
TitleTbUox in complex with uric acid
ComponentsUricase
KeywordsOXIDOREDUCTASE / uricase / urate oxidase
Function / homologyurate oxidase activity / factor-independent urate hydroxylase / Uricase / Uricase / urate catabolic process / purine nucleobase metabolic process / URIC ACID / Uricase
Function and homology information
Biological speciesThermobispora bispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsChiu, Y.C. / Hsu, T.S. / Huang, C.Y. / Hsu, C.H.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2113-M- 002-003 Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2628-B-002-037 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2113-M-002-011 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2628-B-002-013 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural and biochemical insights into a hyperthermostable urate oxidase from Thermobispora bispora for hyperuricemia and gout therapy.
Authors: Chiu, Y.C. / Hsu, T.S. / Huang, C.Y. / Hsu, C.H.
History
DepositionJun 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6174
Polymers68,2802
Non-polymers3362
Water7,873437
1
A: Uricase
B: Uricase
hetero molecules

A: Uricase
B: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2338
Polymers136,5614
Non-polymers6724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area27610 Å2
ΔGint-145 kcal/mol
Surface area40990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.362, 146.362, 132.407
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

21B-545-

HOH

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Components

#1: Protein Uricase / Urate oxidase


Mass: 34140.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) (bacteria)
Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51
Gene: Tbis_2592 / Production host: Escherichia coli (E. coli)
References: UniProt: D6Y599, factor-independent urate hydroxylase
#2: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: sodium cacodylate trihydrate, magnesium acetate tetrahydrate, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→28.58 Å / Num. obs: 38278 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.97 / Net I/σ(I): 92.3
Reflection shellResolution: 2.16→2.23 Å / Num. unique obs: 3502 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OE8

6oe8


Resolution: 2.16→28.58 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 2000 5.22 %
Rwork0.1576 36278 -
obs0.1598 38278 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.67 Å2 / Biso mean: 31.6064 Å2 / Biso min: 12.5 Å2
Refinement stepCycle: final / Resolution: 2.16→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 24 437 5231
Biso mean--31.31 38.26 -
Num. residues----600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.210.26981260.20212284241089
2.21-2.270.26291410.19452563270499
2.27-2.340.27011410.189825512692100
2.34-2.420.24171430.173825942737100
2.42-2.50.23871430.170925942737100
2.5-2.60.22511430.173125882731100
2.6-2.720.22451430.166725962739100
2.72-2.860.23941440.173226162760100
2.86-3.040.23751440.179725972741100
3.04-3.280.21921420.17126052747100
3.28-3.610.18741450.158226262771100
3.61-4.130.16211450.142826312776100
4.13-5.20.13371470.11862663281099
5.2-28.580.17731530.14562770292399
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)
10.18650.10170.18290.0058-0.21280.313-0.0436-0.0505-0.07350.12710.0517-0.0220.1333-0.09320.00260.22070.02250.020.18790.00090.208441.864310.677651.7916
20.2572-0.04360.11730.3634-0.19020.20530.063-0.0789-0.15850.0986-0.00010.00330.10420.0161-00.23850.0387-0.00740.20050.01040.213951.66715.956551.5034
30.0792-0.07110.04990.24910.21260.3334-0.07020.00510.0378-0.00310.00630.09410.0882-0.0459-00.2284-0-0.00330.21440.02890.212345.84980.684244.1868
40.2795-0.2027-0.1120.22070.06120.13780.04080.0691-0.0979-0.04180.01070.03990.15520.0441-00.20990.019-0.00510.1897-0.03080.220449.5466-0.421522.0806
50.2157-0.03520.20920.1667-0.16140.16560.01920.0848-0.0861-0.06880.01010.05720.0623-0.0476-0.00010.15640.0114-0.00790.1345-0.02580.162246.61846.3622.2698
60.1502-0.0403-0.04090.1312-0.30160.4004-0.01470.0452-0.0630.02190.05990.17210.0297-0.1095-00.17840.0242-0.0260.2122-0.01260.21335.77213.561416.4492
70.03530.05220.01270.0975-0.0760.1358-0.1597-0.0471-0.21490.17550.19260.2317-0.0695-0.0648-0.00090.2580.0383-0.00930.2710.01470.240432.799120.145110.9269
80.079-0.0655-0.04810.0802-0.01210.06570.02720.0213-0.15380.08140.0420.1027-0.1014-0.0894-0.00010.19240.0346-0.03640.2118-0.00140.210628.131613.713216.4838
90.0925-0.02360.03440.059-0.00450.0141-0.00510.04650.08370.1779-0.1010.2585-0.0452-0.3461-0.00480.31030.11950.02090.22580.02820.291633.931343.191722.0461
100.227-0.05890.00890.0723-0.16930.37540.02950.0345-0.0058-0.0641-0.09180.1638-0.1188-0.2298-0.00010.19610.0316-0.02460.2656-0.0150.217326.544818.258224.5013
110.30680.0047-0.08970.07470.07830.0955-0.083-0.0878-0.00580.22390.16530.0677-0.0866-0.249-0.00010.30280.05740.04820.2411-0.00860.190235.147623.414558.0977
120.18030.1699-0.0150.09850.01680.06770.1260.01340.03650.0631-0.10340.03750.117-0.30190.00170.15730.06020.01380.3066-0.02770.194123.276424.963535.1665
130.02810.0172-0.03050.0387-0.03270.0496-0.0214-0.1419-0.02630.06160.03240.14470.055-0.282-0.00070.23940.05230.05080.2627-0.00720.235922.875423.068348.0851
140.1268-0.08320.04980.2146-0.0206-0.00030.08440.0567-0.06620.143-0.027-0.00360.1567-0.0040.0010.26280.03320.03460.296-0.01240.236834.99325.048648.5936
150.23340.09180.1346-0.06270.03770.0951-0.026-0.060.00050.0594-0.00570.08590.0042-0.0847-00.20930.02530.00740.2383-0.00110.232833.521818.543943.8087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 56 )A2 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 119 )A57 - 119
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 150 )A120 - 150
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 235 )A151 - 235
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 301 )A236 - 301
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 56 )B2 - 56
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 75 )B57 - 75
8X-RAY DIFFRACTION8chain 'B' and (resid 76 through 103 )B76 - 103
9X-RAY DIFFRACTION9chain 'B' and (resid 104 through 119 )B104 - 119
10X-RAY DIFFRACTION10chain 'B' and (resid 120 through 150 )B120 - 150
11X-RAY DIFFRACTION11chain 'B' and (resid 151 through 180 )B151 - 180
12X-RAY DIFFRACTION12chain 'B' and (resid 181 through 215 )B181 - 215
13X-RAY DIFFRACTION13chain 'B' and (resid 216 through 235 )B216 - 235
14X-RAY DIFFRACTION14chain 'B' and (resid 236 through 259 )B236 - 259
15X-RAY DIFFRACTION15chain 'B' and (resid 260 through 301 )B260 - 301

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