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- PDB-7w7h: S Suis FakA-FakB2 complex structure -

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Basic information

Entry
Database: PDB / ID: 7w7h
TitleS Suis FakA-FakB2 complex structure
Components
  • Predicted kinase related to dihydroxyacetone kinase
  • Uncharacterized protein conserved in bacteria
KeywordsTRANSFERASE / fatty acid kinase / faka / fakb / bacteria
Function / homology
Function and homology information


glycerone kinase activity / glycerol metabolic process / phosphorylation / lipid binding
Similarity search - Function
DAK2 domain-containing protein YloV / Uncharacterised protein, DhaK domain / Fatty acid kinase subunit A-like, C-terminal / Dak1_2 / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / DegV ...DAK2 domain-containing protein YloV / Uncharacterised protein, DhaK domain / Fatty acid kinase subunit A-like, C-terminal / Dak1_2 / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile.
Similarity search - Domain/homology
OLEIC ACID / Uncharacterized protein conserved in bacteria / Predicted kinase related to dihydroxyacetone kinase
Similarity search - Component
Biological speciesStreptococcus suis 05ZYH33 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShi, Y. / Zang, N. / Lou, N. / Xu, Y. / Sun, J. / Huang, M. / Zhang, H. / Lu, H. / Zhou, C. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Sci Adv / Year: 2022
Title: Structure and mechanism for streptococcal fatty acid kinase (Fak) system dedicated to host fatty acid scavenging.
Authors: Shi, Y. / Zang, N. / Lou, N. / Xu, Y. / Sun, J. / Huang, M. / Zhang, H. / Lu, H. / Zhou, C. / Feng, Y.
History
DepositionDec 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Predicted kinase related to dihydroxyacetone kinase
B: Predicted kinase related to dihydroxyacetone kinase
E: Uncharacterized protein conserved in bacteria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,9229
Polymers150,2213
Non-polymers7016
Water1086
1
A: Predicted kinase related to dihydroxyacetone kinase
B: Predicted kinase related to dihydroxyacetone kinase
hetero molecules

E: Uncharacterized protein conserved in bacteria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,9229
Polymers150,2213
Non-polymers7016
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x+1/2,-y-1/2,-z+1/41
Buried area10030 Å2
ΔGint-86 kcal/mol
Surface area56010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.749, 107.749, 398.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 208 or resid 210...
21(chain B and (resid 2 through 208 or resid 210 through 322 or resid 332 through 602))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain A and (resid 2 through 208 or resid 210...AA2 - 2082 - 208
12ASPASPLYSLYS(chain A and (resid 2 through 208 or resid 210...AA210 - 228210 - 228
13ASPASPALAALA(chain A and (resid 2 through 208 or resid 210...AA238 - 322238 - 322
14GLUGLUGLUGLU(chain A and (resid 2 through 208 or resid 210...AA325325
15PROPROZNZN(chain A and (resid 2 through 208 or resid 210...AA - D333 - 601333
21SERSERSERSER(chain B and (resid 2 through 208 or resid 210 through 322 or resid 332 through 602))BB2 - 2082 - 208
22ASPASPALAALA(chain B and (resid 2 through 208 or resid 210 through 322 or resid 332 through 602))BB210 - 322210 - 322
23LYSLYSSO4SO4(chain B and (resid 2 through 208 or resid 210 through 322 or resid 332 through 602))BB - H332 - 602332

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Components

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Protein , 2 types, 3 molecules ABE

#1: Protein Predicted kinase related to dihydroxyacetone kinase / FakA


Mass: 60044.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis 05ZYH33 (bacteria) / Gene: SSU05_1861 / Production host: Escherichia coli (E. coli) / References: UniProt: A4VXI8
#2: Protein Uncharacterized protein conserved in bacteria / FakB2


Mass: 30132.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis 05ZYH33 (bacteria) / Gene: SSU05_1650 / Production host: Escherichia coli (E. coli) / References: UniProt: A4VWX7

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Non-polymers , 4 types, 12 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.4M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→45.261 Å / Num. obs: 73275 / % possible obs: 99.49 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0787 / Rpim(I) all: 0.0285 / Net I/σ(I): 12.13
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.192 / Num. unique obs: 7232 / CC1/2: 0.84 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x9x

4x9x


Resolution: 2.6→45.261 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 6661 4.85 %
Rwork0.1824 130650 -
obs0.1843 73189 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.63 Å2 / Biso mean: 90.3895 Å2 / Biso min: 50 Å2
Refinement stepCycle: final / Resolution: 2.6→45.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10297 0 37 6 10340
Biso mean--96.65 62.74 -
Num. residues----1355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3200X-RAY DIFFRACTION5.917TORSIONAL
12B3200X-RAY DIFFRACTION5.917TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.62960.38441930.33584487100
2.6296-2.66050.32262060.32164312100
2.6605-2.69290.37842320.32164394100
2.6929-2.7270.35431970.30334348100
2.727-2.76290.30742320.27364426100
2.7629-2.80070.29082180.26714310100
2.8007-2.84080.32242430.26584412100
2.8408-2.88310.27152120.26364330100
2.8831-2.92820.35072080.25364415100
2.9282-2.97620.32412110.25194367100
2.9762-3.02750.26132050.24934330100
3.0275-3.08250.30852440.24734398100
3.0825-3.14180.27912180.24994334100
3.1418-3.20590.3132220.24254377100
3.2059-3.27560.31692260.24294411100
3.2756-3.35180.28412310.22144338100
3.3518-3.43560.26162330.21354357100
3.4356-3.52840.26922030.21314374100
3.5284-3.63220.29662030.19654388100
3.6322-3.74940.20632110.18644378100
3.7494-3.88340.23732110.18144401100
3.8834-4.03870.19072430.16434335100
4.0387-4.22240.18622640.15554325100
4.2224-4.44490.16321980.1447433899
4.4449-4.72310.17382810.1435431099
4.7231-5.08730.21452410.1483429898
5.0873-5.59840.23242150.1711431299
5.5984-6.40660.21682110.1881433099
6.4066-8.06410.16882370.1499430198
8.0641-45.2610.17432120.1438421496
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)
13.8467-1.5281-0.21151.33580.21180.934-0.1757-0.0036-0.19370.06470.10590.02590.10210.04290.07040.646-0.0297-0.02040.7841-0.00020.6329109.403-28.30933.622
23.72173.17870.70132.43440.6250.10230.5603-0.6843-0.31830.4704-0.5962-0.23240.2779-0.01610.21480.8744-0.0462-0.02181.0479-0.00010.905675.773-32.43439.996
34.79220.68891.16352.13930.28923.6353-0.13530.2193-0.2032-0.3251-0.01860.05410.472-0.05130.1230.77060.01980.14240.6402-0.05450.585640.238-56.83231.022
41.43731.0436-0.01673.03490.65351.6851-0.1948-0.1832-0.2189-0.1531-0.0409-0.05320.27660.01480.2420.59020.07360.06180.79860.00920.605268.053-38.88515.835
58.0025-1.0513-2.4030.01530.28231.03140.27541.0108-0.0819-0.0536-0.2558-0.3389-0.02430.03050.10170.67640.0018-0.02051.0494-0.0820.768395.93-18.65213.84
63.04640.13491.5842.1603-0.00734.5517-0.06570.29120.35530.034-0.077-0.3479-0.31110.53510.08670.5853-0.0346-0.0070.9040.08770.7351140.357-17.8116.999
71.4174-0.49072.09072.2869-0.99723.5829-0.1201-0.3014-0.33670.07340.13880.04910.7418-0.8833-0.05050.8926-0.12120.22680.90820.04260.818319.84-62.11274.098
81.6595-1.27740.96833.3214-1.11327.023-0.1672-0.2783-0.02710.35250.08520.27990.4411-0.81980.01920.6754-0.07280.12910.7229-0.07630.683724.55-56.16373.361
93.2869-2.5902-1.71896.71754.69958.0188-0.2058-0.21130.15630.29170.1278-0.55190.85040.14370.12020.8176-0.05880.07460.854-0.0140.745933.082-58.34381.599
101.6919-0.73281.34531.4694-0.939.1576-0.0297-0.2856-0.5026-0.3506-0.2698-0.10821.3694-0.33290.30061.3516-0.13040.23620.80590.030.839527.482-73.32678.579
111.14870.2507-0.68471.2825-1.43475.1234-0.03540.0917-0.192-0.0393-0.1131-0.02180.6020.42160.18990.9142-0.00890.12660.7863-0.01020.838336.473-66.82158.661
123.8776-0.69491.20178.0566-1.07595.00760.07120.1501-0.7908-0.3125-0.16810.47181.5347-0.37490.08631.2031-0.14390.19880.7801-0.06680.783626.974-74.32860.519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:305 )A2 - 305
2X-RAY DIFFRACTION2( CHAIN A AND RESID 306:338 )A306 - 338
3X-RAY DIFFRACTION3( CHAIN A AND RESID 339:554 )A339 - 554
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:305 )B2 - 305
5X-RAY DIFFRACTION5( CHAIN B AND RESID 306:338 )B306 - 338
6X-RAY DIFFRACTION6( CHAIN B AND RESID 339:554 )B339 - 554
7X-RAY DIFFRACTION7( CHAIN E AND RESID 1:46 )E1 - 46
8X-RAY DIFFRACTION8( CHAIN E AND RESID 47:94 )E47 - 94
9X-RAY DIFFRACTION9( CHAIN E AND RESID 95:118 )E95 - 118
10X-RAY DIFFRACTION10( CHAIN E AND RESID 119:138 )E119 - 138
11X-RAY DIFFRACTION11( CHAIN E AND RESID 139:218 )E139 - 218
12X-RAY DIFFRACTION12( CHAIN E AND RESID 219:277 )E219 - 277

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