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- PDB-6vdf: Structure of the periplasmic domain of YejM from Salmonella typhi... -

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Basic information

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


hydrolase activity / 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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / O-PHOSPHOETHANOLAMINE / Inner membrane protein YejM / Inner membrane protein YejM
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 25, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,81715
Polymers164,6954
Non-polymers1,12111
Water14,628812
1
A: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5805
Polymers41,1741
Non-polymers4064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2913
Polymers41,1741
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3452
Polymers41,1741
Non-polymers1711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Periplasmic domain of the cardiolipin transporter protein YejM/PbgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6015
Polymers41,1741
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.948, 42.957, 181.209
Angle α, β, γ (deg.)94.280, 94.020, 111.780
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Periplasmic domain of the cardiolipin transporter protein YejM/PbgA / Cardiolipin transport protein PbgA / DUF3413 domain-containing protein / Membrane protein / Sulfatase


Mass: 41173.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: pbgA, yejM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5K1U4E1, UniProt: P40709*PLUS

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Non-polymers , 7 types, 823 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PSE / O-PHOSPHOETHANOLAMINE


Mass: 171.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H10NO5P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 9 % 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: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
Reflection twinOperator: -h,-k,h+k+l / Fraction: 0.45
ReflectionResolution: 1.92→59.9 Å / Num. obs: 70265 / % possible obs: 77.15 % / Redundancy: 1.6 % / CC1/2: 0.971 / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.3
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.7619 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 5489 / CC1/2: 0.191 / Rpim(I) all: 0.7579 / % possible all: 60.59

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VAT

6vat


Resolution: 1.92→59.9 Å / Cross valid method: THROUGHOUT / σ(F): 22.73 / Phase error: 26.7 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2614 3304 5.21 %
Rwork0.2106 66953 -
obs0.22 70265 77.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.46 Å2 / Biso mean: 21.8525 Å2 / Biso min: 6.85 Å2
Refinement stepCycle: final / Resolution: 1.92→59.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10872 0 117 812 11801
Biso mean--49.42 26.25 -
Num. residues----1372
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3152 144 -
Rwork0.2817 2379 -
all-2523 -
obs--52 %
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)
10.4275-0.0518-0.00670.1187-0.00870.0792-0.0504-0.02520.00270.01490.06950.06610.009-0.0270.00280.04740.02940.00390.11690.02520.2234-10.8882-19.8645-4.7296
21.64940.06110.06640.2622-0.07190.5678-0.053-0.1221-0.19060.01990.07870.09950.0176-0.0632-0.01010.05040.00620.02730.1714-0.0040.2135-14.8249-21.59697.3546
31.85050.352-0.01941.95990.24132.0201-0.0743-0.03150.08070.01580.1007-0.169-0.23820.1832-0.01210.063-0.0092-0.01180.2321-0.01620.1106-1.3496-12.224310.6969
40.2591-0.12830.14340.25270.13020.3331-0.0140.0425-0.023-0.078-0.01850.007-0.0626-0.00180.02420.05440.03120.01340.11120.00340.2049-6.16-12.2052-13.6423
50.2258-0.08950.01210.1759-0.06440.21040.06530.0296-0.0548-0.0368-0.0512-0.01930.01850.0206-0.00710.08180.0395-0.0060.10910.00410.256210.054-6.5537-53.3326
62.83121.0446-0.44462.1711-0.54161.1411-0.0350.1482-0.3759-0.0105-0.0159-0.20180.16390.07950.04210.24120.0475-0.02070.0688-0.02860.175510.5218-3.6396-62.7076
70.68730.39750.05162.6370.28852.3980.09660.34040.2963-0.11510.0956-0.0484-0.0850.0418-0.14070.12720.0374-0.00630.13550.04880.189910.61566.1677-66.0464
80.4447-0.0414-0.00360.2036-0.13590.25080.0241-0.05250.00410.0487-0.0278-0.0126-0.0240.02590.02510.07260.0204-0.01510.091-0.01260.252514.62872.4572-41.7471
90.246-0.0401-0.05830.05650.03140.113-0.0217-0.05160.01390.01560.0601-0.0525-0.02180.00840.0020.07880.0601-0.01610.1286-0.00720.2593-0.872311.2403-90.7882
101.44370.9540.04290.813-0.62.16260.0324-0.2286-0.3042-0.03890.1103-0.11350.35710.0773-0.12050.11690.0571-0.01950.22190.01190.2449-9.6662-0.6558-79.6179
110.47750.0384-0.06220.0033-0.01260.68730.0207-0.03570.05130.0017-0.02640.01160.0949-0.0559-0.03050.08030.0592-0.00860.16110.00710.1663-9.66230.0553-92.1399
120.1767-0.1796-0.0360.25-0.10170.2977-0.0160.0089-0.0747-0.0510.0115-0.01080.0462-0.03640.03730.0690.034-0.00210.1083-0.01510.2516-6.67422.4339-106.5919
130.1084-0.02550.02780.0550.00540.07040.02250.02030.01490.0011-0.004-0.0172-0.0306-0.02810.0570.0360.05850.00310.0920.02150.223920.2198-5.9859-139.6785
140.9907-0.8503-0.21221.04030.03491.0060.03160.02750.159-0.0608-0.0414-0.0041-0.1051-0.00620.00370.0980.05590.01860.1170.03480.196419.4123-1.4325-152.2012
151.3864-0.03970.39311.57280.17961.61510.10780.1575-0.120.0466-0.08490.28010.0485-0.2642-0.00090.12620.07550.0330.1528-0.00980.197916.0186-17.3244-155.8292
160.52810.04410.08920.27370.0060.30170.0641-0.07620.04090.0564-0.01310.0494-0.0053-0.0732-0.03530.10620.05250.01050.11260.02450.18114.4589-12.9988-131.4531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 244 through 351 )A244 - 351
2X-RAY DIFFRACTION2chain 'A' and (resid 352 through 408 )A352 - 408
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 436 )A409 - 436
4X-RAY DIFFRACTION4chain 'A' and (resid 437 through 586 )A437 - 586
5X-RAY DIFFRACTION5chain 'B' and (resid 244 through 382 )B244 - 382
6X-RAY DIFFRACTION6chain 'B' and (resid 383 through 412 )B383 - 412
7X-RAY DIFFRACTION7chain 'B' and (resid 413 through 435 )B413 - 435
8X-RAY DIFFRACTION8chain 'B' and (resid 436 through 586 )B436 - 586
9X-RAY DIFFRACTION9chain 'C' and (resid 244 through 399 )C244 - 399
10X-RAY DIFFRACTION10chain 'C' and (resid 400 through 436 )C400 - 436
11X-RAY DIFFRACTION11chain 'C' and (resid 437 through 469 )C437 - 469
12X-RAY DIFFRACTION12chain 'C' and (resid 470 through 586 )C470 - 586
13X-RAY DIFFRACTION13chain 'D' and (resid 244 through 345 )D244 - 345
14X-RAY DIFFRACTION14chain 'D' and (resid 346 through 408 )D346 - 408
15X-RAY DIFFRACTION15chain 'D' and (resid 409 through 436 )D409 - 436
16X-RAY DIFFRACTION16chain 'D' and (resid 437 through 586 )D437 - 586

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