[English] 日本語
Yorodumi
- PDB-8jz4: Crystal structure of AetF in complex with FAD and 5-bromo-L-tryptophan -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jz4
TitleCrystal structure of AetF in complex with FAD and 5-bromo-L-tryptophan
ComponentsAetF
KeywordsFLAVOPROTEIN / halogenase / flavin-dependent / single-component / 5-bromo-L-tryptophan
Function / homologyFAD/NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / 5-bromo-L-tryptophan / FLAVIN-ADENINE DINUCLEOTIDE / AetF
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLi, H. / Dai, L. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and functional insights into the self-sufficient flavin-dependent halogenase.
Authors: Dai, L. / Li, H. / Dai, S. / Zhang, Q. / Zheng, H. / Hu, Y. / Guo, R.T. / Chen, C.C.
History
DepositionJul 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jun 12, 2024Group: Atomic model / Category: atom_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
Description: Model orientation/position
Details: We found that there is a problem with the side chain conformation of the residue Q500. Here, we want to be able to replace the N atom and O atom positions of the residue Q500 side chain.
Provider: author / Type: Coordinate replacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6253
Polymers78,5561
Non-polymers1,0692
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.608, 75.937, 144.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AetF


Mass: 78556.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria)
Gene: aetF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B9Z9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-64X / 5-bromo-L-tryptophan


Mass: 283.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 6000, 0.1 M Tris pH 8.0, 8 mg/mL AetF (5 mM 5-Br-Trp, 5 mM DTT)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.08→25 Å / Num. obs: 39188 / % possible obs: 97.5 % / Redundancy: 3.8 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Χ2: 0.847 / Net I/σ(I): 11 / Num. measured all: 149739
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.08-2.153.80.53337440.8590.9610.3010.6150.59494.8
2.15-2.243.80.36637960.9330.9830.2040.4210.5195.6
2.24-2.343.80.30938090.9480.9870.1760.3570.71996
2.34-2.473.60.19738830.9710.9930.1170.230.63597.5
2.47-2.6240.15639000.9870.9970.0870.1790.70898.6
2.62-2.823.80.11439420.9910.9980.0660.1320.89398.6
2.82-3.114.30.08239730.9950.9990.0440.0930.96999.2
3.11-3.553.90.05339890.9970.9990.030.0611.23399
3.55-4.473.40.03639860.9970.9990.0230.0431.25197.8
4.47-253.70.03341660.9980.9990.0190.0380.92897.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→24.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.282 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26087 1768 5 %RANDOM
Rwork0.19 ---
obs0.19346 33724 88.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.192 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å2-0 Å2
2---0.64 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.08→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5217 0 69 385 5671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135427
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174859
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6517363
X-RAY DIFFRACTIONr_angle_other_deg1.2611.57811262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.135627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24422.074323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89915909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5791538
X-RAY DIFFRACTIONr_chiral_restr0.0690.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021237
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4293.2042520
X-RAY DIFFRACTIONr_mcbond_other2.4293.2042520
X-RAY DIFFRACTIONr_mcangle_it3.6824.7943143
X-RAY DIFFRACTIONr_mcangle_other3.6824.7943144
X-RAY DIFFRACTIONr_scbond_it2.6293.4462907
X-RAY DIFFRACTIONr_scbond_other2.6283.4462908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1935.0564221
X-RAY DIFFRACTIONr_long_range_B_refined6.22637.2666480
X-RAY DIFFRACTIONr_long_range_B_other6.20837.1336409
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.122 Å
RfactorNum. reflection% reflection
Rfree0.301 75 -
Rwork0.257 1435 -
obs--51.61 %

+
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