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- PDB-4wrr: A putative diacylglycerol kinase from Bacillus anthracis str. Sterne -

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Basic information

Entry
Database: PDB / ID: 4wrr
TitleA putative diacylglycerol kinase from Bacillus anthracis str. Sterne
Componentsputative diacylglycerol kinase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Bacillus anthracis / Diacylglycerol kinase / DAGK
Function / homology
Function and homology information


ATP-dependent diacylglycerol kinase activity / phospholipid biosynthetic process / phosphorylation / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
YegS/DAGK, C-terminal domain / Diacylglycerol/lipid kinase / 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 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal ...YegS/DAGK, C-terminal domain / Diacylglycerol/lipid kinase / 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 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsHou, J. / Zheng, H. / Cooper, D.R. / Zimmerman, M.D. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
CitationJournal: to be published
Title: Crystal structure of a putative diacylglycerol kinase from Bacillus anthracis str. Sterne
Authors: Hou, J. / Zheng, H. / Cooper, D.R. / Zimmerman, M.D. / Minor, W.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.6Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative diacylglycerol kinase
B: putative diacylglycerol kinase
C: putative diacylglycerol kinase
D: putative diacylglycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6558
Polymers131,5584
Non-polymers974
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-84 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.099, 138.486, 78.338
Angle α, β, γ (deg.)90.000, 111.480, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSVALVALAA3 - 3003 - 300
21LYSLYSVALVALBB3 - 3003 - 300
12THRTHRALAALAAA4 - 2984 - 298
22THRTHRALAALACC4 - 2984 - 298
13LYSLYSVALVALAA3 - 3003 - 300
23LYSLYSVALVALDD3 - 3003 - 300
14THRTHRALAALABB4 - 2984 - 298
24THRTHRALAALACC4 - 2984 - 298
15LYSLYSVALVALBB3 - 3003 - 300
25LYSLYSVALVALDD3 - 3003 - 300
16THRTHRPROPROCC4 - 2974 - 297
26THRTHRPROPRODD4 - 2974 - 297

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe biological assembly is a dimer.

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Components

#1: Protein
putative diacylglycerol kinase


Mass: 32889.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAK_5150 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: B1EVN9, UniProt: A0A6L8P1L2*PLUS, diacylglycerol kinase (ATP)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium tartrate, 20% PEG3350 in Drop, 1.15M Sodium Chloride in Well

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2014 / Details: MIRROR
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 4.1 % / Number: 272427 / Rmerge(I) obs: 0.088 / Χ2: 0.97 / D res high: 2.16 Å / D res low: 27 Å / Num. obs: 67013 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.842710.0351.1944.2
4.655.8410.0431.254.2
4.064.6510.0461.4344.2
3.694.0610.0551.4694.2
3.433.6910.0571.2654.1
3.233.4310.0671.1014.1
3.063.2310.0881.0354.1
2.933.0610.1110.9774.1
2.822.9310.1320.9034.1
2.722.8210.1560.8544
2.642.7210.1980.8334
2.562.6410.2490.8094
2.492.5610.2760.784
2.432.4910.2960.7614
2.382.4310.3750.7854.1
2.332.3810.4040.7644
2.282.3310.4540.7644
2.242.2810.5250.7474
2.22.2410.5690.7393.9
2.162.210.5640.7373.8
ReflectionResolution: 2.16→27 Å / Num. obs: 67013 / % possible obs: 97.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.049 / Rrim(I) all: 0.101 / Χ2: 0.97 / Net I/av σ(I): 14.8 / Net I/σ(I): 6.8 / Num. measured all: 272427
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.16-2.23.80.56431660.7730.3190.650.73792.8
2.2-2.243.90.56932320.7950.3210.6550.73995.3
2.24-2.2840.52533120.8030.2970.6050.74796.4
2.28-2.3340.45432910.8630.2560.5230.76496.6
2.33-2.3840.40433650.8870.2280.4650.76497.5
2.38-2.434.10.37533100.8940.2110.4310.78598
2.43-2.4940.29633200.9380.1660.340.76197.8
2.49-2.5640.27633630.9470.1540.3170.7897.9
2.56-2.6440.24933450.9470.140.2860.80998.4
2.64-2.7240.19833470.9660.1110.2280.83397.9
2.72-2.8240.15633480.9770.0870.1790.85497.9
2.82-2.934.10.13233660.9850.0730.1520.90397.9
2.93-3.064.10.11133340.9890.0610.1270.97798
3.06-3.234.10.08833640.9930.0480.11.03598.1
3.23-3.434.10.06733520.9950.0370.0771.10197.8
3.43-3.694.10.05733970.9970.0310.0651.26599.1
3.69-4.064.20.05534350.9960.030.0621.46999.9
4.06-4.654.20.04634300.9970.0250.0531.43499.9
4.65-5.844.20.04334530.9980.0240.0491.2599.9
5.84-274.20.03534830.9970.0190.041.19499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5P

3t5p


Resolution: 2.16→27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.684 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 3263 4.9 %RANDOM
Rwork0.2022 63322 --
obs0.2037 63322 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.88 Å2 / Biso mean: 41.376 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20.82 Å2
2---1.09 Å20 Å2
3---0.68 Å2
Refinement stepCycle: final / Resolution: 2.16→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8358 0 4 241 8603
Biso mean--27.9 33.7 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198535
X-RAY DIFFRACTIONr_bond_other_d0.0060.027991
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.95711632
X-RAY DIFFRACTIONr_angle_other_deg1.091318333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34451125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13725.287314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.162151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.716158
X-RAY DIFFRACTIONr_chiral_restr0.0820.21389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219723
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021837
X-RAY DIFFRACTIONr_mcbond_it1.7442.5614545
X-RAY DIFFRACTIONr_mcbond_other1.7442.5614544
X-RAY DIFFRACTIONr_mcangle_it2.7483.8245655
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A160640.08
12B160640.08
21A157030.08
22C157030.08
31A156980.06
32D156980.06
41B156340.07
42C156340.07
51B151790.08
52D151790.08
61C151330.08
62D151330.08
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 244 -
Rwork0.271 4449 -
all-4693 -
obs--93.5 %
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)
11.2726-0.0857-0.58260.63410.14331.02060.04060.0228-0.08140.0766-0.0592-0.0448-0.02380.02470.01850.0124-0.0017-0.00870.06670.02620.24621.073-16.3986.627
21.440.1931-0.56252.1723-1.75253.5533-0.0949-0.0791-0.05930.4391-0.1658-0.0227-0.3165-0.03940.26070.1062-0.02060.0140.0499-0.02190.1475-19.288-20.21124.064
33.5709-0.6494-0.18311.5474-1.9866.3956-0.1092-0.03270.17970.62380.0368-0.0447-1.0241-0.30620.07240.26840.0292-0.02290.0241-0.02310.0883-20.477-11.1823.723
41.1428-0.9197-2.05058.32193.73894.36960.00320.22730.03110.05190.0470.0157-0.0048-0.2469-0.05020.0097-0.0127-0.03050.13870.02380.1306-11.491-14.5223.805
51.04850.1298-0.55740.3717-0.16260.630.03160.007-0.1109-0.0577-0.05490.0279-0.0216-0.03690.02330.01330.0091-0.01170.0875-0.00310.240225.707-15.015-4.88
62.96341.5768-0.33681.2376-1.11657.140.10940.08410.0219-0.2690.04760.09580.2512-0.1311-0.15710.32260.0191-0.06280.1859-0.04660.182434.595-26.1-26.985
71.29020.18620.00662.47510.99083.3923-0.05060.1571-0.1033-0.3911-0.0142-0.0388-0.19070.31550.06480.06470.00030.02410.13910.00010.162949.067-17.711-18.939
82.55390.3402-1.40942.02410.8383.96590.1068-0.10330.1541-0.412-0.04440.1057-0.73130.1874-0.06240.1781-0.0223-0.03110.03190.0190.15842.655-9.627-14.369
91.66230.2101-0.27341.7097-0.57471.22050.10580.00050.12790.1551-0.00370.1537-0.154-0.0336-0.10210.0538-0.00530.08720.0037-0.01860.17584.75215.24510.956
102.5442-1.1778-1.23571.478-0.15871.28930.1921-0.00940.03550.1012-0.07020.2146-0.2337-0.021-0.12190.153-0.01920.09280.0692-0.09030.1973-7.23119.3222.937
113.9086-2.21381.36233.3667-0.17571.90030.0147-0.4354-0.27630.1970.13020.51530.0016-0.128-0.14490.1343-0.05710.17020.077-0.04660.25-16.0717.14933.91
123.1522-1.94610.36171.6095-0.12070.71110.1655-0.1989-0.516-0.03910.01040.4561-0.00710.0996-0.17580.175-0.04090.09730.0805-0.05070.2612-11.62212.18128.87
131.2891-0.3295-0.36941.2937-0.07921.51130.0984-0.06450.15260.0637-0.0318-0.0666-0.08150.0501-0.06660.026-0.00720.05380.0060.00090.193921.30217.747-4.184
144.2238-0.641-0.6531.93921.07111.87120.29590.2389-0.1203-0.0265-0.1013-0.074-0.01140.0006-0.19460.12950.00670.01640.04370.040.174228.44216.47-15.68
153.58613.09941.34334.14413.49616.8660.4210.015-0.16340.1049-0.0639-0.563-0.20310.3542-0.3570.10050.04250.05280.17060.00230.385946.63220.914-17.455
164.80570.95670.63421.46691.13031.91430.22520.6918-0.1549-0.06870.1722-0.3616-0.06810.3139-0.39740.06120.05010.07790.1617-0.00010.220538.87318.551-22.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 129
2X-RAY DIFFRACTION2A130 - 244
3X-RAY DIFFRACTION3A245 - 286
4X-RAY DIFFRACTION4A287 - 300
5X-RAY DIFFRACTION5B3 - 147
6X-RAY DIFFRACTION6B148 - 176
7X-RAY DIFFRACTION7B177 - 245
8X-RAY DIFFRACTION8B246 - 300
9X-RAY DIFFRACTION9C4 - 98
10X-RAY DIFFRACTION10C99 - 183
11X-RAY DIFFRACTION11C184 - 237
12X-RAY DIFFRACTION12C238 - 298
13X-RAY DIFFRACTION13D3 - 115
14X-RAY DIFFRACTION14D116 - 145
15X-RAY DIFFRACTION15D154 - 188
16X-RAY DIFFRACTION16D189 - 300

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