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- PDB-7qar: Serial crystallography structure of cofactor-free urate oxidase i... -

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Basic information

Entry
Database: PDB / ID: 7qar
TitleSerial crystallography structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-methyl uric acid at room temperature
ComponentsUricase
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE / REACTION INTERMEDIATE / SERIAL CRYSTALLOGRAPHY / DIOXYGEN
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / urate catabolic process / peroxisome
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBui, S. / Catapano, L. / Zielinski, K. / Yefanov, O. / Murshudov, G.N. / Oberthuer, D. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P000169/1 United Kingdom
CitationJournal: Iucrj / Year: 2022
Title: Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive.
Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, ...Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, T.A. / Fleckenstein, H. / Sarrou, I. / Werner, N. / Betzel, C. / Rohde, H. / Aepfelbacher, M. / Chapman, H.N. / Perbandt, M. / Steiner, R.A. / Oberthuer, D.
History
DepositionNov 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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
AAA: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5032
Polymers34,2891
Non-polymers2141
Water2,288127
1
AAA: Uricase
hetero molecules

AAA: Uricase
hetero molecules

AAA: Uricase
hetero molecules

AAA: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,0128
Polymers137,1554
Non-polymers8574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area23210 Å2
ΔGint-119 kcal/mol
Surface area44630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.790, 96.030, 105.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11AAA-626-

HOH

21AAA-627-

HOH

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Components

#1: Protein Uricase / Urate oxidase


Mass: 34288.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: Escherichia coli (E. coli)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-XDS / (5S)-5-(dioxidanyl)-9-methyl-7H-purine-2,6,8-trione


Mass: 214.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.6 / Details: TRIS-ACETATE, PEG 8000, MUA,

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→17.07 Å / Num. obs: 18280 / % possible obs: 99.98 % / Redundancy: 28.2 % / CC1/2: 0.849 / CC star: 0.958 / R split: 0.3668 / Net I/σ(I): 2.44
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 20.6 % / Mean I/σ(I) obs: 0.52 / Num. unique obs: 1796 / CC1/2: 0.225 / CC star: 0.606 / R split: 1.9369 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CW2

4cw2


Resolution: 2.3→17.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.576 / SU ML: 0.297 / Cross valid method: FREE R-VALUE / ESU R: 0.309 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2661 919 5.027 %
Rwork0.2182 17361 -
all0.221 --
obs-18280 99.64 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.703 Å2
Baniso -1Baniso -2Baniso -3
1-1.332 Å2-0 Å20 Å2
2---0.446 Å2-0 Å2
3----0.886 Å2
Refinement stepCycle: LAST / Resolution: 2.3→17.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 15 127 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132513
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152336
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0090.013299
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.6473432
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5845400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9315317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47323.015136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08715442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0271513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_nbd_refined0.2030.2374
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21961
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21159
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.222
X-RAY DIFFRACTIONr_nbd_other0.2070.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.216
X-RAY DIFFRACTIONr_mcbond_it1.6123.8341209
X-RAY DIFFRACTIONr_mcbond_other1.6113.831207
X-RAY DIFFRACTIONr_mcangle_it2.8095.7491519
X-RAY DIFFRACTIONr_mcangle_other2.815.7551519
X-RAY DIFFRACTIONr_scbond_it1.5223.991303
X-RAY DIFFRACTIONr_scbond_other1.5223.991302
X-RAY DIFFRACTIONr_scangle_it2.675.8921903
X-RAY DIFFRACTIONr_scangle_other2.675.8921904
X-RAY DIFFRACTIONr_lrange_it4.19573.5014973
X-RAY DIFFRACTIONr_lrange_other4.19473.5214968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.3590.348600.3661274X-RAY DIFFRACTION99.9251
2.359-2.4230.394770.3691193X-RAY DIFFRACTION100
2.423-2.4920.417580.3591204X-RAY DIFFRACTION99.9208
2.492-2.5670.389690.3511144X-RAY DIFFRACTION100
2.567-2.650.401570.3521132X-RAY DIFFRACTION100
2.65-2.7410.417540.3161087X-RAY DIFFRACTION100
2.741-2.8430.343650.3251042X-RAY DIFFRACTION99.9097
2.843-2.9560.286450.2811014X-RAY DIFFRACTION100
2.956-3.0850.31600.258969X-RAY DIFFRACTION100
3.085-3.2310.301510.23932X-RAY DIFFRACTION100
3.231-3.4010.231450.192910X-RAY DIFFRACTION100
3.401-3.6010.241360.179837X-RAY DIFFRACTION100
3.601-3.8410.227420.166803X-RAY DIFFRACTION100
3.841-4.1360.203370.149750X-RAY DIFFRACTION100
4.136-4.5110.191380.129711X-RAY DIFFRACTION100
4.511-5.0120.151310.124628X-RAY DIFFRACTION100
5.012-5.7270.18330.14571X-RAY DIFFRACTION100
5.727-6.8750.233200.169504X-RAY DIFFRACTION100
6.875-9.1930.201270.158397X-RAY DIFFRACTION100
9.193-17.070.243140.185259X-RAY DIFFRACTION91.9192

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