[English] 日本語
Yorodumi
- PDB-7aqu: Flavin-dependent tryptophan halogenase Thal: N-terminally His-tag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aqu
TitleFlavin-dependent tryptophan halogenase Thal: N-terminally His-tagged form of quintuple mutant (NHis-Thal-RebH5)
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / tryptophan halogenase / ThdH / His-Tag
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
ALANINE / GLYCINE / SERINE / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMoritzer, A.C. / Prior, T. / Niemann, H.H.
CitationJournal: Crystals / Year: 2020
Title: Not Cleaving the His-tag of Thal Results in More Tightly Packed and Better-Diffracting Crystals
Authors: Moritzer, A.C. / Prior, T. / Niemann, H.H.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
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)126,06817
Polymers124,7252
Non-polymers1,34315
Water17,565975
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-4 kcal/mol
Surface area38510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.580, 118.570, 87.100
Angle α, β, γ (deg.)90.000, 104.038, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 2 - 529 / Label seq-ID: 22 - 549

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan 6-halogenase


Mass: 62362.312 Da / Num. of mol.: 2 / Mutation: V52I, V82I, S360T, G469S, S470N
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag from pET-28a not cleaved / Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280

-
Non-polymers , 6 types, 990 molecules

#2: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.51 % / Description: Hexagonal
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 9
Details: reservoir solution: 0.1 M bicine pH 9.0, 20 % (w/v) PEG 4000, 10 % (v/v) glycerol, 0.02 M amino acid mix consisting of L-Glu, L-Ala, D-Ala, Gly, L-Lys, D-Lysis, L-Ser and D-Ser; protein ...Details: reservoir solution: 0.1 M bicine pH 9.0, 20 % (w/v) PEG 4000, 10 % (v/v) glycerol, 0.02 M amino acid mix consisting of L-Glu, L-Ala, D-Ala, Gly, L-Lys, D-Lysis, L-Ser and D-Ser; protein buffer solution: 10 mM TRIS, 50 mM NaCl, 1 mM TCEP; protein concentration: ~15 mg/mL; drop ratio: 100 nL+100 nL (protein + reservoir)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2018
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 129082 / % possible obs: 96.6 % / Redundancy: 7.03 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.079 / Net I/σ(I): 15.33
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 6.73 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 8424 / CC1/2: 0.748 / Rrim(I) all: 1.146 / % possible all: 85.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H43 chain A

6h43


Resolution: 1.63→48.579 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.211 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2023 6474 5.017 %
Rwork0.1667 122573 -
all0.168 --
obs-129047 96.564 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.086 Å20 Å2-0.784 Å2
2---0.923 Å20 Å2
3---0.203 Å2
Refinement stepCycle: LAST / Resolution: 1.63→48.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8383 0 88 975 9446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138917
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178068
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.64812115
X-RAY DIFFRACTIONr_angle_other_deg1.4571.5818693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76851098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20321.699512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.837151434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4051567
X-RAY DIFFRACTIONr_chiral_restr0.0840.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022049
X-RAY DIFFRACTIONr_nbd_refined0.220.21809
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.27750
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24457
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2765
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2990.216
X-RAY DIFFRACTIONr_nbd_other0.1960.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.222
X-RAY DIFFRACTIONr_mcbond_it2.3562.6634326
X-RAY DIFFRACTIONr_mcbond_other2.3432.6624325
X-RAY DIFFRACTIONr_mcangle_it3.1973.9745419
X-RAY DIFFRACTIONr_mcangle_other3.1983.9745420
X-RAY DIFFRACTIONr_scbond_it3.0562.974591
X-RAY DIFFRACTIONr_scbond_other3.0542.9694590
X-RAY DIFFRACTIONr_scangle_it4.5814.3396687
X-RAY DIFFRACTIONr_scangle_other4.5794.3396687
X-RAY DIFFRACTIONr_lrange_it6.33832.47510561
X-RAY DIFFRACTIONr_lrange_other6.33932.47810562
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.0518271
Refine LS restraints NCS

Ens-ID: 1 / Number: 18271 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.6720.3044380.2917970X-RAY DIFFRACTION85.2565
1.672-1.7180.2874910.268737X-RAY DIFFRACTION95.8554
1.718-1.7680.2854690.2438524X-RAY DIFFRACTION96.3364
1.768-1.8220.2434460.2268315X-RAY DIFFRACTION96.5293
1.822-1.8820.2554160.2078105X-RAY DIFFRACTION96.7087
1.882-1.9480.2264030.1937811X-RAY DIFFRACTION96.7377
1.948-2.0220.2183710.1787631X-RAY DIFFRACTION97.2178
2.022-2.1040.2183510.1767357X-RAY DIFFRACTION97.3724
2.104-2.1980.2243610.1756994X-RAY DIFFRACTION97.6371
2.198-2.3050.213670.1656707X-RAY DIFFRACTION97.371
2.305-2.4290.23220.1626422X-RAY DIFFRACTION98.0518
2.429-2.5770.2062960.1566161X-RAY DIFFRACTION98.2352
2.577-2.7540.2193210.1545689X-RAY DIFFRACTION98.3633
2.754-2.9750.1853180.155312X-RAY DIFFRACTION98.3578
2.975-3.2580.172730.1474947X-RAY DIFFRACTION98.7701
3.258-3.6420.1772220.1494507X-RAY DIFFRACTION98.9745
3.642-4.2040.1792110.143964X-RAY DIFFRACTION99.1686
4.204-5.1460.1691750.1373343X-RAY DIFFRACTION98.848
5.146-7.2640.2461490.1862611X-RAY DIFFRACTION99.4236
7.264-48.5790.14740.1771466X-RAY DIFFRACTION98.6547

+
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