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- PDB-7zba: HaloTag with Me-TRaQ-G ligand -

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Basic information

Entry
Database: PDB / ID: 7zba
TitleHaloTag with Me-TRaQ-G ligand
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / HaloTag / haloalkane dehalogenase / silicon rhodamine
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-IL7 / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsEmmert, S. / Rivera-Fuentes, P. / Pojer, F. / Lau, K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPCEGP2_186862 Switzerland
Citation
Journal: Nat.Chem. / Year: 2023
Title: A locally activatable sensor for robust quantification of organellar glutathione.
Authors: Emmert, S. / Quargnali, G. / Thallmair, S. / Rivera-Fuentes, P.
#1: Journal: Biorxiv / Year: 2022
Title: A Locally Activatable Sensor for Robust Quantification of Organellar Glutathione
Authors: Hubner, S. / Quargnali, G. / Thallmair, S. / Rivera-Fuentes, P.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Jul 19, 2023Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author / struct_ncs_dom_lim
Item: _audit_author.name / _citation_author.identifier_ORCID ..._audit_author.name / _citation_author.identifier_ORCID / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_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_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_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
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,05915
Polymers68,9472
Non-polymers2,11213
Water8,611478
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4837
Polymers34,4731
Non-polymers1,0106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5768
Polymers34,4731
Non-polymers1,1027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.363, 81.499, 159.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 29 or resid 31...
d_2ens_1(chain "B" and (resid 4 through 29 or resid 31...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILEPROPROAA4 - 294 - 29
d_12ASPASPPHEPHEAA31 - 12831 - 128
d_13ARGARGTRPTRPAA133 - 138133 - 138
d_14GLUGLUALAALAAA140 - 256140 - 256
d_15SERSERPROPROAA258 - 260258 - 260
d_16CYSCYSSERSERAA262 - 284262 - 284
d_17ILEILELEULEUAA286 - 293286 - 293
d_18GOLGOLGOLGOLAC401
d_19GOLGOLGOLGOLAD402
d_110GOLGOLGOLGOLAE403
d_111GOLGOLGOLGOLAF404
d_112IL7IL7IL7IL7AG405
d_21ILEILEPROPROBB4 - 294 - 29
d_22ASPASPPHEPHEBB31 - 13131 - 131
d_23ARGARGTRPTRPBB133 - 138133 - 138
d_24GLUGLUALAALABB140 - 256140 - 256
d_25SERSERPROPROBB258 - 260258 - 260
d_26CYSCYSSERSERBB262 - 284262 - 284
d_27ILEILELEULEUBB286 - 293286 - 293
d_28GOLGOLGOLGOLBJ402
d_29GOLGOLGOLGOLBK403
d_210GOLGOLGOLGOLBL404
d_211GOLGOLGOLGOLBM405
d_212IL7IL7IL7IL7BI401

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 34473.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-IL7 / 4-(7-azanyl-5,5-dimethyl-3-methylimino-benzo[b][1]benzosilin-10-yl)-N-[2-[2-(6-chloranylhexoxy)ethoxy]ethyl]-3-methyl-benzamide / HaloTag with Me-TRaQ-G ligand


Mass: 606.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H44ClN3O3Si / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% v/v PEG smear medium, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 325063 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 14.05 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.09 / Net I/σ(I): 14.16
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 52017 / CC1/2: 0.31 / Rrim(I) all: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Coot0.9.6model building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U32

6u32


Resolution: 1.23→44.56 Å / SU ML: 0.1704 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 8427 5 %
Rwork0.2351 160179 -
obs0.2361 168606 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.23 Å2
Refinement stepCycle: LAST / Resolution: 1.23→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 138 478 5269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544997
X-RAY DIFFRACTIONf_angle_d0.86516829
X-RAY DIFFRACTIONf_chiral_restr0.0708708
X-RAY DIFFRACTIONf_plane_restr0.0072885
X-RAY DIFFRACTIONf_dihedral_angle_d8.5321679
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.23014879656 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.240.36192620.34764995X-RAY DIFFRACTION94.47
1.24-1.260.35622780.33515289X-RAY DIFFRACTION100
1.26-1.270.32462780.31665287X-RAY DIFFRACTION100
1.27-1.290.32762790.3055284X-RAY DIFFRACTION100
1.29-1.310.32152790.29325321X-RAY DIFFRACTION100
1.31-1.320.31552760.28465249X-RAY DIFFRACTION100
1.32-1.340.30332810.27875339X-RAY DIFFRACTION100
1.34-1.360.32772760.27645249X-RAY DIFFRACTION100
1.36-1.380.28882820.27215369X-RAY DIFFRACTION100
1.38-1.410.28942780.26335273X-RAY DIFFRACTION100
1.41-1.430.26042810.25485336X-RAY DIFFRACTION100
1.43-1.460.28722750.2535237X-RAY DIFFRACTION100
1.46-1.490.27452820.25575354X-RAY DIFFRACTION100
1.49-1.520.28452780.25585270X-RAY DIFFRACTION100
1.52-1.550.29222810.24825340X-RAY DIFFRACTION100
1.55-1.580.29352790.2495333X-RAY DIFFRACTION100
1.58-1.620.25542800.23975326X-RAY DIFFRACTION100
1.62-1.670.28122790.23395310X-RAY DIFFRACTION100
1.67-1.720.24112830.23055356X-RAY DIFFRACTION100
1.72-1.770.26092820.23265363X-RAY DIFFRACTION100
1.77-1.840.25442790.22975294X-RAY DIFFRACTION100
1.84-1.910.25562820.22515367X-RAY DIFFRACTION100
1.91-20.23422820.22275347X-RAY DIFFRACTION100
2-2.10.25012840.22275395X-RAY DIFFRACTION100
2.1-2.230.22542830.21795373X-RAY DIFFRACTION100
2.23-2.410.21992840.21755389X-RAY DIFFRACTION100
2.41-2.650.23652850.21835427X-RAY DIFFRACTION100
2.65-3.030.24552870.22215449X-RAY DIFFRACTION100
3.03-3.820.26142890.22795505X-RAY DIFFRACTION100
3.82-44.560.24043030.23395753X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.1134212366 Å / Origin y: -19.0093544721 Å / Origin z: -20.3626778856 Å
111213212223313233
T0.110883033553 Å20.00602946100861 Å20.0103729073961 Å2-0.128554735816 Å20.0244342838694 Å2--0.102055050306 Å2
L0.222993055011 °20.0695288530529 °2-0.0482186582949 °2-0.47525221091 °20.174381436572 °2--0.168142025606 °2
S0.00423523616648 Å °0.0192168400159 Å °0.0203634353087 Å °0.00848911777993 Å °0.00587248510907 Å °0.0226237577542 Å °0.0147838207672 Å °-0.0450262370615 Å °-0.00860862376419 Å °
Refinement TLS groupSelection details: all

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