[English] 日本語
Yorodumi
- PDB-7cu1: CRYSTAL STRUCTURE OF STREPTOMYCES ALBOGRISEOLUS FLAVIN-DEPENDENT ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cu1
TitleCRYSTAL STRUCTURE OF STREPTOMYCES ALBOGRISEOLUS FLAVIN-DEPENDENT TRYPTOPHAN 6-HALOGENASE (THAL) IN COMPLEX WITH FAD and AMP
ComponentsTryptophan 6-halogenase
KeywordsOXIDOREDUCTASE / FLAVIN MONOOXYGENASE / FLAVIN-DEPENDENT TRYPTOPHAN 6-HALOGENASE
Function / homology
Function and homology information


tryptophan 6-halogenase / monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
Model detailsCrystal structure of flavin-dependent tryptophan 6-halogenase (Thal) in complex with FAD from ...Crystal structure of flavin-dependent tryptophan 6-halogenase (Thal) in complex with FAD from Streptomyces albogriseolus
AuthorsChitnumsub, P. / Jaruwat, A. / Phintha, A. / Chaiyen, P.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Dissecting the low catalytic capability of flavin-dependent halogenases.
Authors: Phintha, A. / Prakinee, K. / Jaruwat, A. / Lawan, N. / Visitsatthawong, S. / Kantiwiriyawanitch, C. / Songsungthong, W. / Trisrivirat, D. / Chenprakhon, P. / Mulholland, A. / van Pee, K.H. / ...Authors: Phintha, A. / Prakinee, K. / Jaruwat, A. / Lawan, N. / Visitsatthawong, S. / Kantiwiriyawanitch, C. / Songsungthong, W. / Trisrivirat, D. / Chenprakhon, P. / Mulholland, A. / van Pee, K.H. / Chitnumsub, P. / Chaiyen, P.
History
DepositionAug 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 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: Tryptophan 6-halogenase
B: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,6594
Polymers124,5262
Non-polymers1,1332
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-21 kcal/mol
Surface area38990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.553, 118.151, 82.863
Angle α, β, γ (deg.)90.000, 100.880, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Tryptophan 6-halogenase


Mass: 62263.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280
#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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.14 Å3/Da / Density % sol: 42.66 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: microbatch / pH: 7 / Details: 0.28-0.38M NaF, 23-31% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.91→20.64 Å / Num. obs: 77292 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Net I/σ(I): 16.9 / Num. measured all: 547491
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.465 / Num. measured all: 15402 / Num. unique obs: 3948 / CC1/2: 0.834 / Rpim(I) all: 0.253 / Rrim(I) all: 0.533 / Net I/σ(I) obs: 3.3 / % possible all: 86.2

-
Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HY5

5hy5


Resolution: 1.91→20.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.005 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3807 4.9 %RANDOM
Rwork0.174 ---
obs0.177 73446 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 99.24 Å2 / Biso mean: 17.63 Å2 / Biso min: 5.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0.84 Å2
2---0.35 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.91→20.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8438 0 76 731 9245
Biso mean--23.87 24.27 -
Num. residues----1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0148749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177625
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.66711887
X-RAY DIFFRACTIONr_angle_other_deg0.9411.6417847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96251055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08221.548491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.112151389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5091565
X-RAY DIFFRACTIONr_chiral_restr0.0710.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021750
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 222 -
Rwork0.278 4803 -
all-5025 -
obs--88.75 %

+
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