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- PDB-6vc7: Structure of the F349A mutant of the periplasmic domain of YejM f... -

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Basic information

Entry
Database: PDB / ID: 6vc7
TitleStructure of the F349A mutant of the periplasmic domain of YejM from Salmonella typhimurium
ComponentsPeriplasmic domain of the cardiolipin transporter protein YejM/PbgA
KeywordsHydrolase / Transport protein / YejM / membrane protein / phosphatase / cardiolipin
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall / cardiolipin binding / Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on ester bonds / plasma membrane
Similarity search - Function
Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / : / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
ETHANOLAMINE / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / : / Inner membrane protein PbgA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGabale, U. / Ressl, S.
CitationJournal: Sci Rep / Year: 2020
Title: The essential inner membrane protein YejM is a metalloenzyme.
Authors: Gabale, U. / Pena Palomino, P.A. / Kim, H. / Chen, W. / Ressl, S.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
B: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
C: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
D: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
E: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
F: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,84758
Polymers246,5866
Non-polymers5,26152
Water18,1951010
1
A: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,32714
Polymers41,0981
Non-polymers1,23013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,09711
Polymers41,0981
Non-polymers99910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,01410
Polymers41,0981
Non-polymers9169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7177
Polymers41,0981
Non-polymers6196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8649
Polymers41,0981
Non-polymers7668
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8287
Polymers41,0981
Non-polymers7306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.612, 124.899, 183.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Periplasmic domain of the cardiolipin transporter protein YejM/PbgA


Mass: 41097.707 Da / Num. of mol.: 6 / Mutation: F349A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: pbgA, FKA83_01810 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5A8TP41, UniProt: P40709*PLUS

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Non-polymers , 10 types, 1062 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H7NO
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1010 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1 M HEPES pH 6.8, 5% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.001 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 2.05→43.67 Å / Num. obs: 150136 / % possible obs: 85.9 % / Redundancy: 6.4 % / CC1/2: 0.997 / Net I/σ(I): 13.8
Reflection shellResolution: 2.05→2.123 Å / Num. unique obs: 8464 / CC1/2: 0.184 / % possible all: 48.97

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VAT

6vat


Resolution: 2.05→43.56 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.19
RfactorNum. reflection% reflection
Rfree0.2268 7477 4.98 %
Rwork0.1845 --
obs0.1866 150136 85.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.91 Å2 / Biso mean: 47.2317 Å2 / Biso min: 15.8 Å2
Refinement stepCycle: final / Resolution: 2.05→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16308 0 340 1010 17658
Biso mean--62.56 45.18 -
Num. residues----2064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.070.35341210.32732561268246
2.07-2.10.36831270.31982662278949
2.1-2.120.33961670.31032826299352
2.12-2.150.32621520.29783033318555
2.15-2.180.34951590.28693184334358
2.18-2.210.33421750.28213331350661
2.21-2.240.3331890.26933561375065
2.24-2.270.28691840.25453735391968
2.27-2.310.28361760.24384038421473
2.31-2.350.29532340.23434267450177
2.35-2.390.29182160.22974592480883
2.39-2.430.27532570.22964883514089
2.43-2.480.26933040.22785349565397
2.48-2.530.28322860.208155295815100
2.53-2.580.24993080.2154775785100
2.58-2.640.24453050.207954855790100
2.64-2.710.24692950.207255015796100
2.71-2.780.2773230.222554835806100
2.78-2.860.25562830.204655055788100
2.86-2.960.25852940.197455555849100
2.96-3.060.21752730.198555105783100
3.06-3.180.23342840.194555415825100
3.18-3.330.2422680.193155865854100
3.33-3.50.20142730.174355785851100
3.5-3.720.22392710.161555875858100
3.72-4.010.19952940.153455815875100
4.01-4.420.17833190.139455625881100
4.42-5.050.1743180.124456265944100
5.05-6.360.19413190.164856545973100
6.36-43.670.19283030.16358776180100
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)
12.7271-0.58311.3037.333-0.2432.74980.02840.22460.2268-0.2445-0.12140.44-0.2528-0.24530.09820.10970.04770.02670.32420.00440.1373-35.37436.1617-37.0883
21.8138-0.24330.49452.5170.79961.56350.14810.1638-0.39220.1283-0.13260.23040.2671-0.2687-0.01360.1812-0.0314-0.02470.2707-0.03480.2289-32.371824.0022-30.9198
34.78861.6909-0.90425.49450.69471.90270.1806-0.1318-0.17460.208-0.0830.80640.2325-0.6932-0.22140.2543-0.0888-0.03120.4197-0.1170.4094-43.335916.9748-32.737
42.84570.26030.71941.18440.26321.31250.23520.1895-0.4858-0.0128-0.0543-0.07510.2538-0.0186-0.18830.20160.0206-0.03490.2466-0.06380.2483-22.456722.1806-33.0092
52.4136-2.39173.36382.5767-3.33864.6827-0.2915-0.2090.43560.18870.11960.2274-0.4368-0.28050.21560.245-0.0084-0.06850.2119-0.060.3279-16.601739.2626-24.9851
61.69450.0837-0.97422.8181-0.45362.42160.0184-0.0430.0220.15930.00960.3084-0.1026-0.0601-0.0340.18250.01820.03050.1861-0.00190.1733-58.497139.8777-2.1419
71.4960.2974-0.60782.4635-0.79031.22760.01120.40350.2495-0.28260.15910.50690.0423-0.2824-0.14050.20290.0059-0.0230.31470.07180.2335-61.821744.5444-13.3943
85.78481.85290.41321.7191-1.99574.05810.13780.5695-0.4492-0.63770.01380.59750.0678-0.19510.22820.2229-0.0618-0.05080.31030.06430.2091-67.423937.0576-10.9797
91.17920.6217-0.23772.3782-0.4641.84660.0879-0.02260.28080.27620.02240.4469-0.1144-0.1587-0.04970.19940.01080.07790.19680.01370.2542-60.90742.54670.9692
105.93860.64310.19695.58720.98712.08440.2199-0.17990.55460.41820.00540.2683-0.34120.0137-0.2460.4293-0.06310.15660.20380.00120.365-54.392263.66044.5648
115.228-1.50570.98272.71820.27491.88020.0032-0.3786-0.02390.3820.1158-0.2166-0.09750.1344-0.08740.2846-0.0497-0.03750.11220.01350.20216.002262.2206-2.7643
122.3906-0.21781.04421.60450.75911.8022-0.13660.24070.3649-0.10820.0993-0.2129-0.51560.20470.00540.3492-0.0567-0.01780.18210.03920.26915.341769.2417-13.2954
136.7306-0.2986-0.57185.0386-0.06443.35280.0918-0.19090.5318-0.35010.2269-0.3216-0.72580.4414-0.47120.3335-0.1306-0.03780.2155-0.0290.345312.536670.1094-8.4424
142.20781.8341.25742.68640.21731.30740.00410.0832-0.16050.10470.1813-0.8273-0.21270.4108-0.18570.2412-0.0667-0.10920.2976-0.03450.408918.475560.4682-6.3435
151.1222-0.2488-0.03883.2710.91581.3442-0.0503-0.0353-0.11470.28190.0563-0.03380.00660.027-0.04190.2002-0.007-0.0370.17680.01240.16971.755850.029-7.4103
166.9731-3.5946-2.41222.581-0.20134.91360.08370.13870.24740.24850.03350.5399-0.5984-0.014-0.13560.2203-0.018-0.07710.2156-0.02480.3447-9.032347.4256-16.0175
172.6003-0.3355-0.70512.56891.26822.60590.13170.05740.3586-0.21320.0588-0.1651-0.27730.0272-0.23750.25490.00060.05390.2763-0.01710.20329.618325.5078-54.2059
182.1743-1.3004-1.46217.8281.67126.08940.14150.58630.4696-0.4831-0.07190.6569-0.5437-0.4706-0.03930.4110.1250.10670.34270.05770.3560.170334.3882-56.7957
192.6307-0.63580.17781.88690.69672.1129-0.034-0.42540.31360.22510.1861-0.2423-0.04490.155-0.14190.2814-0.00790.05590.3607-0.09230.242814.089123.7267-42.7991
202.1246-0.5397-0.81953.07910.46493.2560.0046-0.01840.29850.0843-0.0243-0.2126-0.32590.028-0.00150.23670.03810.08570.1964-0.01870.3629-28.225594.1327-0.6351
210.90030.05890.09744.3781.00162.31810.0491-0.25620.36230.25850.1241-0.98560.01410.7121-0.14110.29690.0310.06330.434-0.08560.6382-15.319588.6631-1.3609
224.3905-0.28220.82733.66250.85543.7459-0.0692-0.1010.3353-0.28530.1134-0.8084-0.31220.94470.0330.3506-0.10710.09250.3387-0.16030.6626-15.927797.80551.3757
231.8286-0.201-0.9311.95780.77533.04760.1564-0.11390.39740.13390.061-0.2581-0.477-0.0264-0.13030.36560.04620.08870.1902-0.04890.39-30.257296.45881.9267
246.40151.359-1.5714.32260.62635.28820.0029-0.11680.01330.4625-0.08850.20090.3181-0.42130.11680.3273-0.01230.11710.2384-0.02260.3552-42.742178.86386.7644
252.4832-0.08670.50672.02990.8273.8451-0.025-0.2746-0.0940.28270.1091-0.3980.01770.2423-0.00380.2601-0.0489-0.07740.312-0.10640.381461.8956-3.0434-43.9939
263.4511-0.30611.1211.22750.52712.77720.1614-0.3694-0.69190.20060.0612-0.22620.6252-0.0545-0.25220.3558-0.0468-0.08260.29-0.03450.442755.3776-15.6011-46.3638
274.30760.05073.76064.219-2.11474.4379-0.1489-0.1938-0.71160.1911-0.1944-0.24660.46470.32850.07120.3540.0717-0.17210.2996-0.03570.510363.6843-15.1855-39.9157
282.422-0.48190.45622.26150.65352.6378-0.0386-0.4330.1440.28220.0764-0.1927-0.0564-0.0306-0.01420.2428-0.0566-0.06690.3597-0.0990.308355.94321.9135-39.9869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 243 through 267 )A243 - 267
2X-RAY DIFFRACTION2chain 'A' and (resid 268 through 360 )A268 - 360
3X-RAY DIFFRACTION3chain 'A' and (resid 361 through 409 )A361 - 409
4X-RAY DIFFRACTION4chain 'A' and (resid 410 through 569 )A410 - 569
5X-RAY DIFFRACTION5chain 'A' and (resid 570 through 586 )A570 - 586
6X-RAY DIFFRACTION6chain 'B' and (resid 243 through 292 )B243 - 292
7X-RAY DIFFRACTION7chain 'B' and (resid 293 through 384 )B293 - 384
8X-RAY DIFFRACTION8chain 'B' and (resid 385 through 408 )B385 - 408
9X-RAY DIFFRACTION9chain 'B' and (resid 409 through 526 )B409 - 526
10X-RAY DIFFRACTION10chain 'B' and (resid 527 through 586 )B527 - 586
11X-RAY DIFFRACTION11chain 'C' and (resid 243 through 292 )C243 - 292
12X-RAY DIFFRACTION12chain 'C' and (resid 293 through 386 )C293 - 386
13X-RAY DIFFRACTION13chain 'C' and (resid 387 through 408 )C387 - 408
14X-RAY DIFFRACTION14chain 'C' and (resid 409 through 465 )C409 - 465
15X-RAY DIFFRACTION15chain 'C' and (resid 466 through 569 )C466 - 569
16X-RAY DIFFRACTION16chain 'C' and (resid 570 through 586 )C570 - 586
17X-RAY DIFFRACTION17chain 'D' and (resid 243 through 371 )D243 - 371
18X-RAY DIFFRACTION18chain 'D' and (resid 372 through 408 )D372 - 408
19X-RAY DIFFRACTION19chain 'D' and (resid 409 through 586 )D409 - 586
20X-RAY DIFFRACTION20chain 'E' and (resid 243 through 311 )E243 - 311
21X-RAY DIFFRACTION21chain 'E' and (resid 312 through 384 )E312 - 384
22X-RAY DIFFRACTION22chain 'E' and (resid 385 through 408 )E385 - 408
23X-RAY DIFFRACTION23chain 'E' and (resid 409 through 526 )E409 - 526
24X-RAY DIFFRACTION24chain 'E' and (resid 527 through 586 )E527 - 586
25X-RAY DIFFRACTION25chain 'F' and (resid 243 through 301 )F243 - 301
26X-RAY DIFFRACTION26chain 'F' and (resid 302 through 384 )F302 - 384
27X-RAY DIFFRACTION27chain 'F' and (resid 385 through 411 )F385 - 411
28X-RAY DIFFRACTION28chain 'F' and (resid 412 through 586 )F412 - 586

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  • 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

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