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- PDB-5i5f: Salmonella global domain 191 -

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Basic information

Entry
Database: PDB / ID: 5i5f
TitleSalmonella global domain 191
ComponentsInner membrane protein YejM
KeywordsMEMBRANE PROTEIN / Salmonella 191-586
Function / homologyInner membrane protein YejM / Inner membrane protein YejM, N-terminal / : / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / plasma membrane / Inner membrane protein YejM
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.84 Å
AuthorsDong, C. / Dong, H.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights into cardiolipin transfer from the Inner membrane to the outer membrane by PbgA in Gram-negative bacteria.
Authors: Dong, H. / Zhang, Z. / Tang, X. / Huang, S. / Li, H. / Peng, B. / Dong, C.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Inner membrane protein YejM
B: Inner membrane protein YejM
C: Inner membrane protein YejM
D: Inner membrane protein YejM


Theoretical massNumber of molelcules
Total (without water)268,7864
Polymers268,7864
Non-polymers00
Water17,294960
1
A: Inner membrane protein YejM


Theoretical massNumber of molelcules
Total (without water)67,1961
Polymers67,1961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inner membrane protein YejM


Theoretical massNumber of molelcules
Total (without water)67,1961
Polymers67,1961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Inner membrane protein YejM


Theoretical massNumber of molelcules
Total (without water)67,1961
Polymers67,1961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Inner membrane protein YejM


Theoretical massNumber of molelcules
Total (without water)67,1961
Polymers67,1961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.570, 195.880, 70.090
Angle α, β, γ (deg.)90.00, 95.75, 90.00
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: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 243 - 585 / Label seq-ID: 243 - 585

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Inner membrane protein YejM


Mass: 67196.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: yejM, STM2228 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40709
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-tris pH 6.5 and 25% PEG3350 / PH range: 6.2-6.7

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Data collection

DiffractionMean temperature: 191 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.84→65.7 Å / % possible obs: 99.4 % / Redundancy: 5.4 % / Net I/σ(I): 5.8
Reflection shellResolution: 1.84→1.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.84→65.7 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.212 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24403 5005 4.9 %RANDOM
Rwork0.1653 ---
obs0.1692 97804 86.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.112 Å2
Baniso -1Baniso -2Baniso -3
1--15.64 Å20 Å2-34.88 Å2
2---28.4 Å20 Å2
3---44.03 Å2
Refinement stepCycle: LAST / Resolution: 1.84→65.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 0 960 11684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910976
X-RAY DIFFRACTIONr_bond_other_d0.0120.0210124
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.93314940
X-RAY DIFFRACTIONr_angle_other_deg1.783323156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21851348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17324.46556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.886151644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0071568
X-RAY DIFFRACTIONr_chiral_restr0.1360.21660
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212724
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022744
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0442.6795416
X-RAY DIFFRACTIONr_mcbond_other6.042.6785415
X-RAY DIFFRACTIONr_mcangle_it7.2674.0166756
X-RAY DIFFRACTIONr_mcangle_other7.274.0166757
X-RAY DIFFRACTIONr_scbond_it7.0693.1635560
X-RAY DIFFRACTIONr_scbond_other7.0693.1635561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.284.568185
X-RAY DIFFRACTIONr_long_range_B_refined9.30723.42313493
X-RAY DIFFRACTIONr_long_range_B_other9.17523.15413107
X-RAY DIFFRACTIONr_rigid_bond_restr3.726321100
X-RAY DIFFRACTIONr_sphericity_free39.1915291
X-RAY DIFFRACTIONr_sphericity_bonded20.638521518
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A411740.08
12B411740.08
21A408500.09
22C408500.09
31A412340.08
32D412340.08
41B409860.09
42C409860.09
51B412240.08
52D412240.08
61C419480.06
62D419480.06
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 181 -
Rwork0.315 3565 -
obs--42.83 %
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)
10.0252-0.0119-0.00880.0274-0.01370.01830.00180.00190.00410.0051-0.0010.00150.0003-0.004-0.00080.07550.00010.04850.1190.00030.031471.6024-31.11625.6979
20.03620.0009-0.02880.1385-0.01870.02630.0042-0.00550.00840.0013-0.00010.0040.0023-0.0034-0.00420.07990.00110.04910.1288-0.00020.03194.0201-31.019339.1989
30.0844-0.03550.03540.0590.01430.0375-0.00170.0075-0.00460.00530.00590.0044-0.00360.0018-0.00420.0843-0.00140.05040.1175-0.00140.030382.0483-74.6748-7.9151
40.03-0.03620.00260.0724-0.03140.0281-0.0079-0.0108-0.00370.01310.00660.0026-0.0050.00330.00130.0882-0.00320.05110.1192-0.00160.0302104.2429-74.927827.1385
50.00390.00230.00060.00140.00040.0002-0.0001-0.0040.00030.0021-0.00060.00120.00240.00170.00070.09220.00070.05570.1319-0.00030.033787.0623-54.048313.8243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 585
2X-RAY DIFFRACTION2B243 - 585
3X-RAY DIFFRACTION3C243 - 585
4X-RAY DIFFRACTION4D243 - 585
5X-RAY DIFFRACTION5Z1 - 961

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