[English] 日本語
Yorodumi
- PDB-4uyo: Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uyo
TitleStructure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18 angstrom resolution
ComponentsDIACYLGLYCEROL KINASE-DELTA 7
KeywordsTRANSFERASE / 7.9 MAG / IN MESO CRYSTALLIZATION / LIPID CUBIC PHASE / LIPIDIC CUBIC PHASE / LIPID MESOPHASE / LIPIDIC MESOPHASE / MEMBRANE PROTEIN / MICROCRYSTALS / MONOACYLGLYCEROL / ROOM TEMPERATURE CRYSTALLOGRAPHY / SERIAL FEMTOSECOND CRYSTALLOGRAPHY / X-RAY FREE-ELECTRON LASER
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / lipid kinase activity / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #3610 / DAGK family / Diacylglycerol kinase, prokaryotic / Diacylglycerol kinase (DAGK) superfamily / Prokaryotic diacylglycerol kinase / Prokaryotic diacylglycerol kinase signature. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K12 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLi, D. / Howe, N. / Other, O. / Caffrey, M.
CitationJournal: Nat.Commun. / Year: 2015
Title: Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase.
Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / ...Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / Weierstall, U. / Zatsepin, N.A. / Cherezov, V. / Liu, W. / Bandaru, S. / English, N.J. / Gati, C. / Barty, A. / Yefanov, O. / Chapman, H.N. / Diederichs, K. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Marvin Seibert, M. / Caffrey, M.
History
DepositionSep 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 1.3Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIACYLGLYCEROL KINASE-DELTA 7
B: DIACYLGLYCEROL KINASE-DELTA 7
C: DIACYLGLYCEROL KINASE-DELTA 7
D: DIACYLGLYCEROL KINASE-DELTA 7
E: DIACYLGLYCEROL KINASE-DELTA 7
F: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,43817
Polymers85,2276
Non-polymers3,21111
Water1,53185
1
A: DIACYLGLYCEROL KINASE-DELTA 7
B: DIACYLGLYCEROL KINASE-DELTA 7
C: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2568
Polymers42,6133
Non-polymers1,6425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DIACYLGLYCEROL KINASE-DELTA 7
E: DIACYLGLYCEROL KINASE-DELTA 7
F: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1829
Polymers42,6133
Non-polymers1,5686
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.300, 91.800, 141.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
DIACYLGLYCEROL KINASE-DELTA 7 / DAGK / DIGLYCERIDE KINASE / DGK / DIACYLGLYCEROL KINASE-DELTA7


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K12 (bacteria) / Plasmid: PTRCHISB-DGKA-DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

-
Non-polymers , 5 types, 96 molecules

#2: Chemical
ChemComp-79N / (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H36O4
#3: Chemical
ChemComp-79M / (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / [(2R)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H36O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 140440

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 % / Description: R SPLIT (I) 0.07, R SPLIT FOR SHELL (I) 2.38
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: 0.2 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 20 DEGREES CELCIUS WITH THE 7. ...Details: 0.2 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 20 DEGREES CELCIUS WITH THE 7.9 MONOACYLGLYCEROL (7.9 MAG) AS THE HOSTING LIPID.CRYSTALLIZATION WAS SET UP BY INCUBATING 20 MICROLITERS OF LIPID CUBIC PHASE WITH 400 MICROLITERS OF PRECIPITANT SOLUTION IN COUPLED SYRINGES.

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.302 / Wavelength: 1.302 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Mar 25, 2013
RadiationMonochromator: K-B MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.302 Å / Relative weight: 1
ReflectionResolution: 2.18→40.5 Å / Num. obs: 54058 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 3466 % / Biso Wilson estimate: 71.31 Å2 / Net I/σ(I): 19
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 3519 % / Mean I/σ(I) obs: 0.44 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZE3

3ze3


Resolution: 2.18→40.013 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 28.73 / Stereochemistry target values: ML
Details: THERE ARE SIX NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2362 2583 5 %
Rwork0.2076 --
obs0.209 51797 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.42 Å2
Refinement stepCycle: LAST / Resolution: 2.18→40.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 221 85 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085244
X-RAY DIFFRACTIONf_angle_d0.9497132
X-RAY DIFFRACTIONf_dihedral_angle_d13.9631927
X-RAY DIFFRACTIONf_chiral_restr0.057855
X-RAY DIFFRACTIONf_plane_restr0.003873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.22190.38671450.37722591X-RAY DIFFRACTION96
2.2219-2.26730.34151360.35632676X-RAY DIFFRACTION99
2.2673-2.31660.38811500.34462681X-RAY DIFFRACTION100
2.3166-2.37050.39251260.33292737X-RAY DIFFRACTION100
2.3705-2.42970.36231580.31262700X-RAY DIFFRACTION100
2.4297-2.49540.33191510.29712686X-RAY DIFFRACTION100
2.4954-2.56880.3231600.26932707X-RAY DIFFRACTION100
2.5688-2.65170.25791470.23852694X-RAY DIFFRACTION100
2.6517-2.74650.27371300.2172715X-RAY DIFFRACTION100
2.7465-2.85640.26891500.2012723X-RAY DIFFRACTION100
2.8564-2.98640.24261410.19322738X-RAY DIFFRACTION100
2.9864-3.14380.25981460.18812760X-RAY DIFFRACTION100
3.1438-3.34060.2651450.19622722X-RAY DIFFRACTION100
3.3406-3.59840.23671290.18682783X-RAY DIFFRACTION100
3.5984-3.96030.22871310.17712771X-RAY DIFFRACTION100
3.9603-4.53260.16311330.15482792X-RAY DIFFRACTION100
4.5326-5.7080.23471610.21632798X-RAY DIFFRACTION100
5.708-40.01970.23441440.232940X-RAY DIFFRACTION99

+
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