[English] 日本語
Yorodumi
- PDB-4qgm: Acireductone dioxygenase from Bacillus anthracis with cadmium ion... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qgm
TitleAcireductone dioxygenase from Bacillus anthracis with cadmium ion in active center
ComponentsAcireductone dioxygenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / RmlC-like cupin / Iron Binding / 1 / 2-dihydroxy-5-(methylthio)pent-1-en-3-one dioxygenase
Function / homology
Function and homology information


acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / nickel cation binding / iron ion binding
Similarity search - Function
Acireductone dioxygenase ARD, bacteria / Acireductone dioxygenase ARD family / ARD/ARD' family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Acireductone dioxygenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsMilaczewska, A.M. / Chruszcz, M. / Shabalin, I.G. / Cooper, D.R. / Borowski, T. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Acireductone dioxygenase from Bacillus anthracis with cadmium ion in active center
Authors: Milaczewska, A.M. / Chruszcz, M. / Shabalin, I.G. / Cooper, D.R. / Borowski, T. / Minor, W.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acireductone dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9562
Polymers19,8431
Non-polymers1121
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.215, 49.522, 33.349
Angle α, β, γ (deg.)90.00, 99.95, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Acireductone dioxygenase / 1 / 2-dihydroxy-3-keto-5-methylthiopentene dioxygenase / DHK-MTPene dioxygenase / Acireductone ...1 / 2-dihydroxy-3-keto-5-methylthiopentene dioxygenase / DHK-MTPene dioxygenase / Acireductone dioxygenase (Fe(2+)-requiring) / ARD' / Fe-ARD / Acireductone dioxygenase (Ni(2+)-requiring) / ARD / Ni-ARD


Mass: 19843.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS3949, BA_4258, GBAA4258, GBAA_4258, mtnD / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus DE3 RIPL
References: UniProt: Q81MI9, acireductone dioxygenase [iron(II)-requiring], acireductone dioxygenase (Ni2+-requiring)
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein: 5.5mg/ml, in 50 mM Tris-HCl pH 7.8, 150mM NaCl, 1mM CdCl, Crystallization condition: 62% Tacsimate pH=9.0, 0.0075M CdCl2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2012 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 3560 / Num. obs: 3560 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 57.37 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 11.046
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.919 / Num. unique all: 179 / Rsym value: 0.473 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000MOLREPphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vr3
Resolution: 2.97→52.31 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 41.973 / SU ML: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23423 152 4.3 %RANDOM
Rwork0.18386 ---
obs0.1861 3386 97.57 %-
all-3386 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.763 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å2-0.35 Å2
2--0.1 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2.97→52.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 1 14 1368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191382
X-RAY DIFFRACTIONr_bond_other_d0.0060.02889
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9331881
X-RAY DIFFRACTIONr_angle_other_deg0.86632175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6615172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30424.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4815219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.79156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02279
LS refinement shellResolution: 2.967→3.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 5 -
Rwork0.257 171 -
obs-171 69.84 %
Refinement TLS params.Method: refined / Origin x: -15.611 Å / Origin y: -24.407 Å / Origin z: 1.367 Å
111213212223313233
T0.0838 Å20.0027 Å20.0034 Å2-0.0715 Å20.0459 Å2--0.0523 Å2
L1.5752 °20.2701 °2-0.1169 °2-4.1329 °21.7692 °2--2.9704 °2
S-0.05 Å °-0.0027 Å °-0.0661 Å °0.1627 Å °0.0659 Å °0.0795 Å °0.0967 Å °0.1365 Å °-0.0159 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 170
2X-RAY DIFFRACTION1A301 - 314

+
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