[English] 日本語
Yorodumi
- PDB-8ful: Heterologous AibH1H2 purified from Lysogeny broth -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ful
TitleHeterologous AibH1H2 purified from Lysogeny broth
Components(Amidohydrolase) x 3
KeywordsOXIDOREDUCTASE / alpha aminoisobutyric acid hydroxylase amidohydrolase-like dimetallic
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
: / Amidohydrolase / Amidohydrolase
Similarity search - Component
Biological speciesRhodococcus wratislaviensis NBRC 100605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsPowell, M.M. / Rittle, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor.
Authors: Powell, M.M. / Rao, G. / Britt, R.D. / Rittle, J.
History
DepositionJan 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amidohydrolase
B: Amidohydrolase
C: Amidohydrolase
D: Amidohydrolase
E: Amidohydrolase
F: Amidohydrolase
G: Amidohydrolase
H: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,96823
Polymers345,0898
Non-polymers87915
Water10,683593
1
A: Amidohydrolase
B: Amidohydrolase
E: Amidohydrolase
F: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,99612
Polymers172,5454
Non-polymers4518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19650 Å2
ΔGint-100 kcal/mol
Surface area42130 Å2
MethodPISA
2
C: Amidohydrolase
D: Amidohydrolase
G: Amidohydrolase
H: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,97211
Polymers172,5454
Non-polymers4277
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19850 Å2
ΔGint-109 kcal/mol
Surface area42100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.772, 231.403, 144.997
Angle α, β, γ (deg.)90.000, 92.169, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-503-

HOH

31A-565-

HOH

41E-560-

HOH

-
Components

-
Protein , 3 types, 8 molecules ACEGBDFH

#1: Protein
Amidohydrolase


Mass: 43992.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis NBRC 100605 (bacteria)
Gene: Rhow_000804 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A402C2V4
#2: Protein Amidohydrolase


Mass: 42272.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis NBRC 100605 (bacteria)
Gene: Rhow_000803 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A402C2Q3
#3: Protein Amidohydrolase


Mass: 42288.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis NBRC 100605 (bacteria)
Gene: Rhow_000803 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A402C2Q3

-
Non-polymers , 4 types, 608 molecules

#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M MgCl2, 0.08 M HEPES, 20% PEG4000, 20% glycerol, 10 mM sodium dithionite

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2021
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→47.28 Å / Num. obs: 119391 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 46.15 Å2 / CC1/2: 0.989 / Net I/σ(I): 8.1
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 3.1 % / Num. unique obs: 11704 / CC1/2: 0.915 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M2I

6m2i


Resolution: 2.29→47.28 Å / SU ML: 0.4089 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6543 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2579 2000 1.68 %
Rwork0.1904 117391 -
obs0.1915 119391 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.56 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22606 0 25 593 23224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008623355
X-RAY DIFFRACTIONf_angle_d1.056331930
X-RAY DIFFRACTIONf_chiral_restr0.05673416
X-RAY DIFFRACTIONf_plane_restr0.00784218
X-RAY DIFFRACTIONf_dihedral_angle_d11.113519067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.45841400.40418202X-RAY DIFFRACTION96
2.35-2.410.41351360.31518235X-RAY DIFFRACTION96.42
2.41-2.480.38021420.27418257X-RAY DIFFRACTION96.82
2.48-2.560.34951400.2668317X-RAY DIFFRACTION97.05
2.56-2.650.31281430.23568287X-RAY DIFFRACTION97.28
2.65-2.760.2911400.21068370X-RAY DIFFRACTION97.51
2.76-2.890.29211460.2098361X-RAY DIFFRACTION98.01
2.89-3.040.30351420.20218379X-RAY DIFFRACTION98.18
3.04-3.230.24671420.19218426X-RAY DIFFRACTION98.32
3.23-3.480.26531450.17988420X-RAY DIFFRACTION98.54
3.48-3.830.22021380.16418476X-RAY DIFFRACTION98.64
3.83-4.380.2051490.16218476X-RAY DIFFRACTION98.94
4.38-5.520.22731510.1678552X-RAY DIFFRACTION99.5
5.52-47.280.23431460.16868633X-RAY DIFFRACTION99.82

+
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