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- PDB-5z27: Crystal structure of highly active BTUO mutant P287G without dehy... -

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Basic information

Entry
Database: PDB / ID: 5z27
TitleCrystal structure of highly active BTUO mutant P287G without dehydration
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: 1.6 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
DepositionDec 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)74,76510
Polymers74,1352
Non-polymers6298
Water9,764542
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)149,52920
Polymers148,2704
Non-polymers1,25916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area25420 Å2
ΔGint-81 kcal/mol
Surface area41290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.496, 133.047, 144.717
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: 37067.594 Da / Num. of mol.: 2 / Mutation: p287G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (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, 550 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.28 Å3/Da / Density % sol: 45.66 %
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: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 85987 / % possible obs: 95.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.04 / Rrim(I) all: 0.088 / Net I/σ(I): 15.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4405 / CC1/2: 0.676 / Rpim(I) all: 0.322 / Rrim(I) all: 0.664 / Χ2: 1

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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: 1.6→45.35 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1787 1996 2.32 %
Rwork0.163 --
obs0.1634 85973 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 40 542 5254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064881
X-RAY DIFFRACTIONf_angle_d0.8426635
X-RAY DIFFRACTIONf_dihedral_angle_d9.3692847
X-RAY DIFFRACTIONf_chiral_restr0.054741
X-RAY DIFFRACTIONf_plane_restr0.006844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5996-1.63960.2771410.23735992X-RAY DIFFRACTION96
1.6396-1.6840.24941440.22196117X-RAY DIFFRACTION98
1.684-1.73350.23461400.20626079X-RAY DIFFRACTION98
1.7335-1.78950.21391670.18596048X-RAY DIFFRACTION98
1.7895-1.85350.20561310.18596088X-RAY DIFFRACTION97
1.8535-1.92770.22671310.17986065X-RAY DIFFRACTION97
1.9277-2.01540.18711510.16716013X-RAY DIFFRACTION97
2.0154-2.12160.20151430.15986036X-RAY DIFFRACTION97
2.1216-2.25460.1821380.14895990X-RAY DIFFRACTION96
2.2546-2.42860.15761460.1485975X-RAY DIFFRACTION95
2.4286-2.6730.17571420.14915933X-RAY DIFFRACTION95
2.673-3.05970.16011380.15655890X-RAY DIFFRACTION93
3.0597-3.85460.15041410.15325853X-RAY DIFFRACTION92
3.8546-45.36840.16681430.1595898X-RAY DIFFRACTION90
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)
10.5820.12450.07281.6898-0.30940.8542-0.0210.2258-0.0532-0.37040.00610.04780.0009-0.1031-0.00960.2162-0.0143-0.02840.2368-0.06530.1805-8.4097-14.8544-53.4155
20.7109-0.0575-0.47870.8305-0.11112.9449-0.03750.0973-0.1363-0.0373-0.03250.06310.1714-0.19350.06720.1543-0.0325-0.01380.1532-0.05720.2082-11.2249-24.7566-37.0185
30.94180.0075-0.85723.4373-3.45794.33790.02920.1659-0.2548-0.11820.04720.07620.1919-0.0567-0.08820.178-0.0244-0.04260.1608-0.06470.2127-15.411-25.1534-46.1149
40.3644-0.0983-0.06720.2154-0.00890.38090.01240.1482-0.0608-0.1270.00940.05910.0376-0.0478-0.0280.1412-0.0183-0.02120.1657-0.00660.1374-12.0289-6.4404-47.8634
50.5425-0.1843-0.05682.10790.64491.43930.05660.2065-0.0316-0.2919-0.02140.1548-0-0.1122-0.03020.1603-0.013-0.05160.2390.02040.1532-18.64553.1013-54.092
60.7748-0.06830.36880.90650.3281.92160.03390.08050.0571-0.0861-0.140.1998-0.0247-0.14410.11070.11560.0092-0.01290.16830.0110.1605-16.00377.7225-45.955
70.1712-0.15530.16240.7529-0.98952.5752-0.0136-0.01530.02280.01120.02870.0035-0.0013-0.1095-0.03990.1090.0105-0.00060.15240.00520.142-15.57497.1106-15.3312
80.7218-0.3660.5380.6934-0.33232.12070.00430.09280.0561-0.02380.01190.1098-0.0554-0.1412-0.01260.10820.0088-0.00940.13870.03670.1528-24.345312.6986-29.64
90.2641-0.043-0.16010.8662-0.06630.42050.0270.018-0.03290.07790.01620.0426-0.0138-0.0095-0.05280.0914-0.0053-0.00010.10460.00970.0973-11.24-2.5421-19.2054
100.8727-0.7931-0.29541.46350.94861.4415-0.0185-0.0142-0.09940.03140.0610.03790.042-0.0575-0.0420.1167-0.01840.01130.11580.01980.136-13.6585-11.3121-15.235
114.867-3.5348-4.54134.3863.91466.2845-0.1304-0.0312-0.23910.1630.04660.08440.3083-0.05760.10290.1395-0.0205-0.00120.10640.01780.1505-16.9633-17.5032-13.5685
120.93940.0959-0.40240.43310.16960.8403-0.0730.0894-0.244-0.01510.0274-0.04160.07910.02110.05510.1549-0.01090.00040.1484-0.01610.1872-7.5273-16.1064-23.1286
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 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 263 )
6X-RAY DIFFRACTION6chain 'A' and (resid 264 through 310 )
7X-RAY DIFFRACTION7chain 'B' and (resid 8 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 192 )
10X-RAY DIFFRACTION10chain 'B' and (resid 193 through 248 )
11X-RAY DIFFRACTION11chain 'B' and (resid 249 through 263 )
12X-RAY DIFFRACTION12chain 'B' and (resid 264 through 310 )

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