[English] 日本語
Yorodumi
- PDB-5z27: Crystal structure of highly active BTUO mutant P287G without dehy... -

+
Open data


ID or keywords:

Loading...

-
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 activity / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / factor-independent urate hydroxylase / urate oxidase activity / allantoin metabolic process / urate catabolic process / purine nucleobase metabolic process / peroxisome
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more