[English] 日本語
Yorodumi
- PDB-4brb: Crystal structure of the integral membrane enzyme DgkA-ref, delta 7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4brb
TitleCrystal structure of the integral membrane enzyme DgkA-ref, delta 7
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / LIPID METABOLISM / MEMBRANE PROTEIN
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)-PENTADEC-7-ENOATE / ACETATE ION / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLi, D. / Caffrey, M.
CitationJournal: Sci.Rep. / Year: 2014
Title: Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic.
Authors: Li, D. / Caffrey, M.
History
DepositionJun 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: 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)88,68519
Polymers85,2276
Non-polymers3,45813
Water37821
1
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,12911
Polymers42,6133
Non-polymers2,5168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-83.2 kcal/mol
Surface area15770 Å2
MethodPISA
2
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5568
Polymers42,6133
Non-polymers9425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-113.3 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.500, 91.570, 143.570
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 / DIACYLGLYCEROL KINASE -DELTA 7


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTRCHISB-DGKA-DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

-
Non-polymers , 5 types, 34 molecules

#2: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer details(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78N)
Sequence detailsTHE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE ...THE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS SEVEN MUTATIONS. THEY ARE A41C, C46A, I53V, I70L, M96L, V107D AND C113A.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.43 % / Description: NONE
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M 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 7.8 MONOACYLGLYCEROL (7.8 MAG) AS THE HOSTING LIPID.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03319
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.55→71.79 Å / Num. obs: 32610 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 55.99 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.2 / % possible all: 97.9

-
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: 2.55→45.233 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 27.42 / 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
Rfree0.2614 1634 5 %
Rwork0.2173 --
obs0.2196 32531 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.43 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 238 21 4762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014806
X-RAY DIFFRACTIONf_angle_d1.0556506
X-RAY DIFFRACTIONf_dihedral_angle_d14.2031732
X-RAY DIFFRACTIONf_chiral_restr0.064803
X-RAY DIFFRACTIONf_plane_restr0.003771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6250.31971380.2782528X-RAY DIFFRACTION98
2.625-2.70970.27461410.23452564X-RAY DIFFRACTION99
2.7097-2.80660.25441290.2272561X-RAY DIFFRACTION99
2.8066-2.91890.26941220.20692561X-RAY DIFFRACTION99
2.9189-3.05180.24331240.20292594X-RAY DIFFRACTION99
3.0518-3.21260.24551550.20342544X-RAY DIFFRACTION99
3.2126-3.41380.28471410.21542581X-RAY DIFFRACTION99
3.4138-3.67730.31941330.27482470X-RAY DIFFRACTION95
3.6773-4.04720.26631350.21962455X-RAY DIFFRACTION94
4.0472-4.63230.20271430.16772637X-RAY DIFFRACTION99
4.6323-5.83420.25821280.2222664X-RAY DIFFRACTION99
5.8342-45.24030.27381450.2262738X-RAY DIFFRACTION98
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)
15.5344-1.7846-1.22832.61961.44055.654-0.2364-0.16740.53430.30570.1297-0.0169-0.3029-0.05080.04870.3668-0.07270.00280.36420.00150.421439.635330.376514.4951
26.49813.1981-4.92853.8073-4.6415.94430.06330.1708-0.0176-0.0881-0.4303-0.27850.18510.43420.44940.32720.04420.02150.22360.00820.292432.959424.89316.998
36.1812-0.86740.61727.25151.86653.55840.2374-0.9824-0.79761.33370.15740.50590.8706-0.245-0.54020.6189-0.13290.0730.45390.09970.413127.696112.453625.0446
45.32562.17821.42682.7330.23790.4469-0.87970.45150.3678-1.61560.0128-1.08591.25070.95560.82290.72130.20330.21160.53840.05810.474835.739818.0974-4.0318
53.9595-3.91752.53386.7311.22347.5684-0.4765-0.29630.11330.33910.07520.0802-0.4079-0.27070.13970.3042-0.016-0.04490.34730.01720.401618.086136.31515.7642
66.2142-1.24731.74326.9476-5.28064.0942-0.236-0.7470.36481.1850.1606-0.2483-1.6007-0.95470.0220.42470.05630.05070.3544-0.0110.431722.455327.58224.9112
74.27120.5598-0.67464.5433-5.86067.48650.0276-0.2420.17660.97810.0557-0.2851-1.3521.24460.04170.4141-0.0285-0.02440.2937-0.0560.357432.065129.047823.5369
83.6831.56640.10416.16396.88448.4806-0.12520.8896-0.2987-0.26930.2217-0.6935-1.62550.32540.07590.3743-0.1069-0.04560.35190.05320.381830.222138.9336-2.1218
97.94382.01021.25294.60835.26216.4534-0.0773-2.7832-0.35711.19090.4772-0.6781.38830.0427-0.0670.87620.0266-0.24720.99470.13460.900816.0578.63784.9479
106.52781.5098-0.11742.53410.28746.23280.26170.7334-0.617-0.6135-0.6465-0.1140.66020.40890.58340.53740.1308-0.05360.385-0.00770.423522.009617.3524-5.7542
112.98793.0966-4.02743.4141-4.50587.38780.4795-0.4941-0.33861.0925-0.05710.5173-0.1513-1.4369-0.92260.5528-0.0097-0.01180.4920.10470.417120.086916.724818.8531
123.87020.05511.74263.01390.78487.47050.1294-0.5752-0.10490.43070.31380.33610.1074-1.046-0.49420.19190.04160.01090.41380.03190.392214.866823.471511.4686
139.819-2.82441.56327.44884.05084.4102-0.36570.84350.0632-0.01320.21630.0052-0.30360.31340.12950.3305-0.05840.02070.28910.03960.18430.234737.3709-17.8188
149.1541-0.63891.20588.7596-1.11766.1454-0.3363-0.7205-0.24841.1628-0.2582-0.0118-0.67190.11650.6170.50330.01890.00060.29790.04610.35074.864442.22352.0464
157.47862.4046-3.86462.2754-1.49627.30130.10570.4832-0.093-0.13840.0042-0.81560.49971.33760.08750.57160.102-0.02210.55550.03630.53799.251248.091-25.5931
167.4308-0.6993-0.37427.2932-3.71791.9344-0.4791-0.6647-0.16970.8372-0.4958-0.5114-0.53340.73350.85770.4087-0.0317-0.0490.363-0.02910.356312.926548.9919-1.5611
171.996-8.27761.76276.8955-1.03381.4195-1.028-1.08210.42810.76210.719-0.3480.12760.0067-0.19351.19770.60250.86271.29170.9173.2337-13.355560.2474-2.9379
186.5491-0.8956-0.37547.01430.84070.1103-0.2972-0.95040.49941.2847-0.49480.5992-2.3671-3.20910.48241.05210.48010.06461.1601-0.06130.5394-6.29758.01483.4051
197.4492-0.44134.90657.56460.29153.3105-0.03011.0601-0.6475-0.3561-0.05260.29480.4956-0.4148-0.03750.4214-0.02630.07790.57430.07540.5354-3.113250.8339-27.238
208.6153-2.7865-7.7775.4713.85719.12920.2944-0.7923-0.07110.6587-0.0703-0.09610.0594-0.7768-0.34730.3189-0.0507-0.01090.55030.05930.2046-7.059247.3426-1.2933
212.4636-0.7013-0.18474.3581-4.13544.49470.71490.50380.8550.17830.11680.7429-2.67143.2104-0.11761.4326-0.4565-0.09231.1330.00741.023216.819864.8519-4.7362
222.6222-0.89910.25453.3189-2.49731.9167-0.1823-0.10050.09250.1728-0.1385-0.2638-1.51810.51010.23840.3334-0.0790.00350.30440.0030.42727.475457.7215-15.025
234.26662.72233.17863.55154.34675.442-0.33790.15250.39790.2543-0.09290.7343-2.0242-0.4190.24041.10560.3187-0.02130.35690.0080.4626-0.369762.8966-17.3791
246.22511.48264.36620.36671.21175.7132-0.2001-1.76851.78761.51440.089-0.1238-1.198-0.3446-0.08671.79140.1-0.08230.4452-0.38250.54722.476567.17875.6034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:49)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 50:76)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 77:103)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 104:121)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 24:64)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 65:85)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 86:106)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 107:120)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 31:41)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 42:65)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 66:80)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 81:121)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 14:32)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 33:65)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 66:93)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 94:121)
17X-RAY DIFFRACTION17(CHAIN E AND RESID 35:46)
18X-RAY DIFFRACTION18(CHAIN E AND RESID 47:65)
19X-RAY DIFFRACTION19(CHAIN E AND RESID 66:95)
20X-RAY DIFFRACTION20(CHAIN E AND RESID 96:120)
21X-RAY DIFFRACTION21(CHAIN F AND RESID 29:48)
22X-RAY DIFFRACTION22(CHAIN F AND RESID 49:89)
23X-RAY DIFFRACTION23(CHAIN F AND RESID 90:107)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 108:120)

+
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://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