[English] 日本語
Yorodumi
- PDB-4wvz: Crystal structure of artificial crosslinked thiol dioxygenase G95... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wvz
TitleCrystal structure of artificial crosslinked thiol dioxygenase G95C variant from Pseudomonas aeruginosa
Components3-mercaptopropionate dioxygenase
KeywordsOXIDOREDUCTASE / thiol dioxygenase / cysteine dioxygenase / 3-MPA dioxygenase / 3-mercaptopropionic acid / non-heme mono-iron / Cupin / beta barrel / crosslink
Function / homology
Function and homology information


3-mercaptopropionate dioxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding / iron ion binding
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RmlC-like jelly roll fold / Jelly Rolls / Up-down Bundle / Sandwich ...ATP synthase delta/epsilon subunit, C-terminal domain / Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RmlC-like jelly roll fold / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Thiol dioxygenase / 3-mercaptopropionate dioxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsFellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M.
CitationJournal: Biochemistry / Year: 2016
Title: Substrate and pH-Dependent Kinetic Profile of 3-Mercaptopropionate Dioxygenase from Pseudomonas aeruginosa.
Authors: Fellner, M. / Aloi, S. / Tchesnokov, E.P. / Wilbanks, S.M. / Jameson, G.N.
History
DepositionNov 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Dec 30, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _audit_author.name / _citation.journal_id_CSD ..._audit_author.name / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-mercaptopropionate dioxygenase
B: 3-mercaptopropionate dioxygenase
C: 3-mercaptopropionate dioxygenase
D: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5188
Polymers95,2954
Non-polymers2234
Water10,088560
1
A: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.543, 66.543, 376.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
3-mercaptopropionate dioxygenase / Thiol dioxygenase


Mass: 23823.666 Da / Num. of mol.: 4 / Mutation: G95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA2602 / Plasmid: pPR-IBA1/PA2602/P.aeruginosa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9I0N5, UniProt: A0A140UH61*PLUS, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 2.5microl Protein at 18 mg/ml (in 10mM phosphate pH 7.5) was mixed with 1microl of the mother liquor containing 140mM sodiumacetate, PEG 4000 8%, pH 5.3, the reservoir contained 500microl. ...Details: 2.5microl Protein at 18 mg/ml (in 10mM phosphate pH 7.5) was mixed with 1microl of the mother liquor containing 140mM sodiumacetate, PEG 4000 8%, pH 5.3, the reservoir contained 500microl. Cryoprotected with 25% ethylenglycol before freezing.

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.09→47.05 Å / Num. obs: 51753 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Net I/σ(I): 28.1 / Num. measured all: 359980
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.09-2.153.70.2824.21422138500.9150.15796.9
9.11-47.056.20.01666486178110.00798.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.89 Å47.05 Å
Translation7.89 Å47.05 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.8data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TLF

4tlf


Resolution: 2.09→39.914 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 2548 4.95 %
Rwork0.1753 88465 -
obs0.1775 51609 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.47 Å2 / Biso mean: 35.5237 Å2 / Biso min: 14.46 Å2
Refinement stepCycle: final / Resolution: 2.09→39.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 4 560 6890
Biso mean--52 41.94 -
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066630
X-RAY DIFFRACTIONf_angle_d1.0029035
X-RAY DIFFRACTIONf_chiral_restr0.039938
X-RAY DIFFRACTIONf_plane_restr0.0051217
X-RAY DIFFRACTIONf_dihedral_angle_d13.8122462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.11380.33751450.25492482262784
2.1138-2.13860.28591370.24222719285687
2.1386-2.16470.26321370.23512620275788
2.1647-2.19210.27231650.232760292591
2.1921-2.2210.28831480.23722866301493
2.221-2.25140.39151450.3562582272788
2.2514-2.28360.41061540.27092831298592
2.2836-2.31760.29031900.21072886307698
2.3176-2.35380.25351580.188330563214100
2.3538-2.39240.26761410.195630333174100
2.3924-2.43370.26131570.192629923149100
2.4337-2.47790.28241540.201930993253100
2.4779-2.52560.24881650.198329793144100
2.5256-2.57710.24371510.182230403191100
2.5771-2.63320.21511480.18330493197100
2.6332-2.69440.22641570.188230493206100
2.6944-2.76180.28621410.175130593200100
2.7618-2.83640.28451490.175829763125100
2.8364-2.91980.24951320.180731273259100
2.9198-3.01410.27971540.189530173171100
3.0141-3.12170.23011340.181530323166100
3.1217-3.24670.23041440.173330613205100
3.2467-3.39440.20721830.171229983181100
3.3944-3.57320.16421530.163330163169100
3.5732-3.79690.19711830.16482976315999
3.7969-4.08980.18381380.141130973235100
4.0898-4.50090.1721730.137329973170100
4.5009-5.1510.15271670.131530213188100
5.151-6.48520.1891650.161730153180100
6.4852-39.92090.15961360.15993030316699

+
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://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