[English] 日本語
Yorodumi
- PDB-4brr: Crystal structure of the integral membrane diacylglycerol kinase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4brr
TitleCrystal structure of the integral membrane diacylglycerol kinase - delta 7.79
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / DGKA / IN MESO CRYSTALLIZATION / LOW TEMPERATURE CRYSTALLIZATION / MEMBRANE PROTEIN / LCP / LIPIDIC CUBIC PHASE / LIPID MESOPHASE
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / phosphorylation / ATP binding / identical protein binding / membrane / metal ion binding / 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 / ACETATE ION / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsLi, D. / Howe, N. / Caffrey, M.
CitationJournal: To be Published
Title: Crystal Structure of an Integral Membrane Enzyme Determined by X-Ray Free Electron Laser Femtocrystallography
Authors: Li, D. / Howe, N. / Caffrey, M.
History
DepositionJun 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: 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
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,52612
Polymers85,2276
Non-polymers1,2996
Water1086
1
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2705
Polymers42,6133
Non-polymers6572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-69.1 kcal/mol
Surface area19570 Å2
MethodPISA
2
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2557
Polymers42,6133
Non-polymers6424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-56 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.060, 91.500, 143.720
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 / DAGK / DIGLYCERIDE KINASE / DGK


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PTRCHISB-DGKA-DELTA 7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

-
Non-polymers , 5 types, 12 molecules

#2: 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.: 3 / Source method: obtained synthetically / Formula: C19H36O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.47 % / Description: NONE
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 60 MM MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 60 MM MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 7.9 MONOACYLGLYCEROL (7.9 MAG) AS THE HOSTING LIPID.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03315
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.44→75.06 Å / Num. obs: 37160 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 51.52 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.6
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

-
Processing

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

3ze3


Resolution: 2.44→66.533 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 28.12 / Stereochemistry target values: ML
Details: THERE ARE THREE NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT THE NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2522 1847 5 %
Rwork0.2178 --
obs0.2195 37090 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.27 Å2
Refinement stepCycle: LAST / Resolution: 2.44→66.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 87 6 4563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074627
X-RAY DIFFRACTIONf_angle_d0.6886307
X-RAY DIFFRACTIONf_dihedral_angle_d11.4281603
X-RAY DIFFRACTIONf_chiral_restr0.045798
X-RAY DIFFRACTIONf_plane_restr0.002751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.5060.35861330.32572692X-RAY DIFFRACTION99
2.506-2.57970.34661210.28382704X-RAY DIFFRACTION99
2.5797-2.6630.28131570.2562671X-RAY DIFFRACTION99
2.663-2.75820.29661310.24422672X-RAY DIFFRACTION99
2.7582-2.86860.26141310.2282707X-RAY DIFFRACTION99
2.8686-2.99920.25961470.21632670X-RAY DIFFRACTION98
2.9992-3.15730.23531500.20762687X-RAY DIFFRACTION99
3.1573-3.35510.23581490.21422698X-RAY DIFFRACTION99
3.3551-3.61410.25321470.2062711X-RAY DIFFRACTION99
3.6141-3.97780.23031460.19712711X-RAY DIFFRACTION98
3.9778-4.55330.2221520.17412728X-RAY DIFFRACTION99
4.5533-5.73610.27881370.22422754X-RAY DIFFRACTION98
5.7361-66.55740.24231460.23212838X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.9694-5.6009-2.41014.90350.88124.9972-0.9183-0.79120.68140.89110.7454-0.3926-0.9082-0.48230.18170.6210.027-0.04350.7282-0.16610.3962-1.2586-11.539722.5959
24.7179-0.6920.34141.75921.74541.9708-0.1985-0.05840.05450.12680.026-0.19860.2974-0.23360.18730.2860.00630.01360.35610.00840.306-1.0176-21.35439.4533
37.92211.347-1.83146.9886-0.22350.43940.216-0.1245-0.0809-0.0318-0.1082-0.08350.2235-0.23470.14240.330.0587-0.03820.2504-0.10460.3812-6.2389-31.31029.7274
48.6312-1.79010.97899.05621.21117.3647-0.3585-1.16250.25711.09160.45460.6849-1.1619-0.64-0.16030.42770.13450.00480.54470.02530.6381-21.7865-7.46498.8024
53.85341.0415-0.05573.107-1.51885.90440.0019-0.13030.16590.44120.160.0568-0.8305-0.049-0.15850.34410.05660.01380.2212-0.02860.315-10.8741-14.406213.8918
67.61023.9816-2.74963.6614-4.04626.62090.42340.7768-1.2747-0.7271-0.7924-0.339-0.04930.08230.62460.83110.0785-0.19350.4939-0.18990.7983-19.5387-33.5442-4.427
73.5363-0.67931.4162.5949-0.29758.47350.1404-0.4389-0.09790.33120.07960.32080.3064-0.6576-0.17150.321-0.07490.00990.40340.05250.3159-20.0418-24.407110.5227
82.95960.83441.43485.3467-0.41163.721-0.08460.0846-0.13210.10090.0752-0.0306-0.14180.03530.02270.33820.06760.02330.40020.0390.3302-33.9663-3.9623-9.657
95.54810.3168-1.2225.2216-4.09168.6125-0.2560.1179-0.01630.0804-0.3489-0.4164-0.38020.93160.61320.31960.0048-0.09140.37710.00230.4905-24.20083.8292-9.9552
101.49760.58430.66280.91550.48040.5339-0.6892-0.94351.24810.42510.09450.60990.0802-0.34140.5150.56240.65890.30051.69390.37961.7086-50.384513.9220.8099
113.44981.33221.06092.9263-0.63171.79430.10620.11860.21170.01980.04830.1002-0.5201-1.2106-0.15480.3920.14930.01330.47840.06370.3774-42.37595.0068-12.5078
122.53443.0404-3.04563.6499-3.65543.6635-0.5137-0.9797-0.16890.379-0.5882-1.4067-1.44280.32890.90381.3318-0.134-0.13481.06640.01241.1224-22.559918.52450.9444
132.1316-0.8374-0.22042.9141-2.47997.92450.20530.0706-0.1483-0.02950.0893-0.0534-1.14320.6098-0.37310.421-0.03810.01960.369-0.02040.4442-30.514511.6421-17.5436
146.99031.33120.99195.00123.34053.7187-0.2001-0.69510.57780.2155-0.0262-0.0461-2.3101-1.02360.32830.85630.2025-0.06970.37550.01170.4824-36.66119.2626-5.9159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 8 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28 THROUGH 82 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 83 THROUGH 121 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 23 THROUGH 51 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 52 THROUGH 120 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 33 THROUGH 51 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 52 THROUGH 121 )
8X-RAY DIFFRACTION8CHAIN D AND (RESID 14 THROUGH 82 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 83 THROUGH 121 )
10X-RAY DIFFRACTION10CHAIN E AND (RESID 34 THROUGH 51 )
11X-RAY DIFFRACTION11CHAIN E AND (RESID 52 THROUGH 120 )
12X-RAY DIFFRACTION12CHAIN F AND (RESID 33 THROUGH 51 )
13X-RAY DIFFRACTION13CHAIN F AND (RESID 52 THROUGH 90 )
14X-RAY DIFFRACTION14CHAIN F AND (RESID 91 THROUGH 120 )

+
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://pdbjlvh1.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