[English] 日本語
Yorodumi
- PDB-2qv7: Crystal Structure of Diacylglycerol Kinase DgkB in complex with A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qv7
TitleCrystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg
ComponentsDiacylglycerol Kinase DgkB
KeywordsTRANSFERASE / alpha-beta domain 1 / beta sandwich domain 2 / Protein-ADP complex
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phospholipid biosynthetic process / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Diacylglycerol/lipid kinase / YegS/DAGK, C-terminal domain / YegS C-terminal NAD kinase beta sandwich-like domain / Tumour Suppressor Smad4 - #40 / : / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 ...Diacylglycerol/lipid kinase / YegS/DAGK, C-terminal domain / YegS C-terminal NAD kinase beta sandwich-like domain / Tumour Suppressor Smad4 - #40 / : / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Diacylglycerol kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement of DgkB / Resolution: 2.3 Å
AuthorsMiller, D.J. / Jerga, A. / Rock, C.O. / White, S.W.
CitationJournal: Structure / Year: 2008
Title: Analysis of the Staphylococcus aureus DgkB Structure Reveals a Common Catalytic Mechanism for the Soluble Diacylglycerol Kinases.
Authors: Miller, D.J. / Jerga, A. / Rock, C.O. / White, S.W.
History
DepositionAug 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diacylglycerol Kinase DgkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3513
Polymers37,8991
Non-polymers4522
Water2,738152
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Diacylglycerol Kinase DgkB
hetero molecules

A: Diacylglycerol Kinase DgkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7016
Polymers75,7982
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)123.760, 123.760, 47.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Diacylglycerol Kinase DgkB


Mass: 37899.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAR1989 / Plasmid: pAJ015 / Production host: Escherichia coli (E. coli) / Strain (production host): methionine auxotroph B834 / References: UniProt: Q6GFF9, diacylglycerol kinase (ATP)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: drop: 0.1 M Tris pH 8.5, 9% PEG2K MME; well: 0.1 M Tris pH 8.5, 18% PEG2K MME, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2007 / Details: mirrors
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 17025 / Num. obs: 16997 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rsym value: 0.128 / Net I/σ(I): 24.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1667 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
DgkBmodel used for rigid body refinementphasing
RefinementMethod to determine structure: Rigid body refinement of DgkB
Resolution: 2.3→29.17 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.497 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 857 5.1 %RANDOM
Rwork0.20648 ---
obs0.20845 16069 99.58 %-
all-16997 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.138 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 28 152 2504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222393
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9853240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92925.093108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5231511
X-RAY DIFFRACTIONr_chiral_restr0.0610.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021801
X-RAY DIFFRACTIONr_nbd_refined0.1770.21050
X-RAY DIFFRACTIONr_nbtor_refined0.30.21583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.211
X-RAY DIFFRACTIONr_mcbond_it0.431.51542
X-RAY DIFFRACTIONr_mcangle_it0.67622388
X-RAY DIFFRACTIONr_scbond_it1.0933953
X-RAY DIFFRACTIONr_scangle_it1.6034.5852
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 81 -
Rwork0.218 1130 -
obs--99.34 %
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)
12.0622-1.748-0.23762.88030.10331.34440.1358-0.0014-0.0199-0.0425-0.0911-0.0721-0.0260.0218-0.0447-0.096-0.0286-0.0305-0.05490.0365-0.104457.359439.697521.3913
215.681-4.5687.46193.9168-2.05159.4463-0.2467-0.68250.07520.34560.1075-0.0115-0.21631.00350.1392-0.10610.0341-0.00680.20710.0912-0.073681.378225.749932.2201
36.997-0.88240.68121.03190.19190.3777-0.0669-0.3633-0.4159-0.0507-0.01180.03780.23780.05580.0787-0.0420.0383-0.0131-0.08410.0724-0.081980.620619.048624.3563
47.39620.30191.15218.6303-2.06016.08060.04920.3618-0.1648-0.28520.07250.2903-0.1564-0.0423-0.12170.0080.07690.0515-0.05520.0114-0.149591.755922.54717.5372
57.9025-1.49240.34374.01660.48752.111-0.1975-1.1044-0.54860.39380.19360.09060.150.02480.004-0.10430.0492-0.0183-0.01930.1247-0.116173.788419.282929.7515
610.3742-4.18524.075217.2624-5.9468.71370.53591.9443-0.0013-1.1273-0.4027-0.01580.07860.5026-0.13310.00330.1568-0.05670.1301-0.035-0.218264.064829.36053.584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2A135 - 144
3X-RAY DIFFRACTION3A166 - 200
4X-RAY DIFFRACTION3A207 - 229
5X-RAY DIFFRACTION4A230 - 249
6X-RAY DIFFRACTION5A250 - 286
7X-RAY DIFFRACTION6A296 - 312

+
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