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- PDB-3s40: The crystal structure of a diacylglycerol kinases from Bacillus a... -

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Basic information

Entry
Database: PDB / ID: 3s40
TitleThe crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne
Componentsdiacylglycerol kinase
KeywordsTRANSFERASE / diacylglycerol kinases / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ATP-dependent diacylglycerol kinase activity / phospholipid biosynthetic process / ATP binding / metal ion binding / plasma membrane
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
BmrU protein / BmrU protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTan, K. / Zhang, R. / Xu, X. / Cui, H. / Peterson, S. / Savchenko, A. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne
Authors: Tan, K. / Zhang, R. / Xu, X. / Cui, H. / Peterson, S. / Savchenko, A. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: diacylglycerol kinase
B: diacylglycerol kinase
C: diacylglycerol kinase
D: diacylglycerol kinase


Theoretical massNumber of molelcules
Total (without water)133,4784
Polymers133,4784
Non-polymers00
Water5,927329
1
A: diacylglycerol kinase


Theoretical massNumber of molelcules
Total (without water)33,3691
Polymers33,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: diacylglycerol kinase


Theoretical massNumber of molelcules
Total (without water)33,3691
Polymers33,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: diacylglycerol kinase


Theoretical massNumber of molelcules
Total (without water)33,3691
Polymers33,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: diacylglycerol kinase


Theoretical massNumber of molelcules
Total (without water)33,3691
Polymers33,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-39 kcal/mol
Surface area44260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.608, 130.758, 72.794
Angle α, β, γ (deg.)90.00, 115.04, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is predicted that the molecule is monomeric.

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Components

#1: Protein
diacylglycerol kinase


Mass: 33369.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS4713, BA_5075, GBAA_5075 / Plasmid: p15Tv Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81KC6, UniProt: A0A6L8P1L2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M Bis-Tris, 0.4M NH4Cl, 16% PEG 3350, 4% Jeffamine M-600, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.1→44 Å / Num. all: 62575 / Num. obs: 62575 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QVL

2qvl


Resolution: 2.1→43.231 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 2979 5.07 %
Rwork0.1746 --
obs0.1778 58777 93.6 %
all-58777 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.943 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1946 Å2-0 Å20.4934 Å2
2--0.2684 Å2-0 Å2
3---3.9262 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8600 0 0 329 8929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078776
X-RAY DIFFRACTIONf_angle_d1.07711902
X-RAY DIFFRACTIONf_dihedral_angle_d15.3333171
X-RAY DIFFRACTIONf_chiral_restr0.0751382
X-RAY DIFFRACTIONf_plane_restr0.0051528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0997-2.13420.35271300.26042181X-RAY DIFFRACTION77
2.1342-2.1710.29711340.2382378X-RAY DIFFRACTION84
2.171-2.21040.31391220.20942432X-RAY DIFFRACTION86
2.2104-2.2530.30541340.19742453X-RAY DIFFRACTION87
2.253-2.29890.22221430.19312491X-RAY DIFFRACTION89
2.2989-2.34890.24481270.18542581X-RAY DIFFRACTION90
2.3489-2.40360.28951490.19522523X-RAY DIFFRACTION90
2.4036-2.46370.26051380.19052624X-RAY DIFFRACTION92
2.4637-2.53030.28351390.192617X-RAY DIFFRACTION93
2.5303-2.60470.25131560.19332667X-RAY DIFFRACTION95
2.6047-2.68880.32471280.19622717X-RAY DIFFRACTION95
2.6888-2.78490.24541560.19782704X-RAY DIFFRACTION96
2.7849-2.89630.29011530.19552764X-RAY DIFFRACTION97
2.8963-3.02810.30721430.21612793X-RAY DIFFRACTION98
3.0281-3.18770.28231320.18852818X-RAY DIFFRACTION98
3.1877-3.38740.22181670.18262769X-RAY DIFFRACTION99
3.3874-3.64880.21921560.16432847X-RAY DIFFRACTION100
3.6488-4.01580.20781440.14732820X-RAY DIFFRACTION100
4.0158-4.59630.17781580.14192848X-RAY DIFFRACTION100
4.5963-5.78860.19491400.14352880X-RAY DIFFRACTION100
5.7886-43.24060.21791300.16382891X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.7048 Å / Origin y: 33.0817 Å / Origin z: 37.1669 Å
111213212223313233
T0.1217 Å2-0.0028 Å2-0.0224 Å2-0.0942 Å20.0153 Å2--0.0958 Å2
L0.5572 °20.0478 °2-0.1427 °2-0.1781 °2-0.0095 °2--0.3274 °2
S0.0603 Å °-0.016 Å °-0.0759 Å °0.0355 Å °-0.0313 Å °-0.0081 Å °-0.0823 Å °0.0137 Å °-0.0009 Å °
Refinement TLS groupSelection details: all

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