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- PDB-8em5: Mycobacterium thermoresistible MmpS5 -

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Basic information

Entry
Database: PDB / ID: 8em5
TitleMycobacterium thermoresistible MmpS5
ComponentsMmpS5
KeywordsPROTEIN BINDING / periplasmic protein
Function / homologyTransport accessory protein MmpS / Transport accessory protein MmpS, C-terminal / Mycobacterium membrane protein / IODIDE ION / Uncharacterized protein
Function and homology information
Biological speciesMycolicibacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsCuthbert, B.J. / Goulding, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Metallomics / Year: 2024
Title: The structure of Mycobacterium thermoresistibile MmpS5 reveals a conserved disulfide bond across mycobacteria.
Authors: Cuthbert, B.J. / Mendoza, J. / de Miranda, R. / Papavinasasundaram, K. / Sassetti, C.M. / Goulding, C.W.
History
DepositionSep 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MmpS5
B: MmpS5
C: MmpS5
D: MmpS5
E: MmpS5
F: MmpS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,33338
Polymers65,7796
Non-polymers6,55432
Water9,836546
1
A: MmpS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2098
Polymers10,9631
Non-polymers1,2457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MmpS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2415
Polymers10,9631
Non-polymers1,2774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MmpS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4026
Polymers10,9631
Non-polymers1,4395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MmpS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9486
Polymers10,9631
Non-polymers9855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MmpS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9707
Polymers10,9631
Non-polymers1,0076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: MmpS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5636
Polymers10,9631
Non-polymers6005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.284, 85.257, 89.124
Angle α, β, γ (deg.)90.000, 95.190, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
MmpS5


Mass: 10963.166 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile (bacteria)
Gene: KEK_05752 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CDU2

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Non-polymers , 5 types, 578 molecules

#2: Chemical
ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris pH 6.5, 25% PEG3350
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→40.08 Å / Num. obs: 51815 / % possible obs: 95 % / Redundancy: 4.3 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.079 / Rrim(I) all: 0.162 / Χ2: 0.86 / Net I/σ(I): 7.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3435 / CC1/2: 0.713 / Rpim(I) all: 0.455 / Rrim(I) all: 0.969 / Χ2: 0.67 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→40.08 Å / SU ML: 0.1748 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1941 5176 10 %
Rwork0.1612 46592 -
obs0.1645 51768 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.95 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 226 546 4894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094489
X-RAY DIFFRACTIONf_angle_d1.05596096
X-RAY DIFFRACTIONf_chiral_restr0.0734743
X-RAY DIFFRACTIONf_plane_restr0.0104761
X-RAY DIFFRACTIONf_dihedral_angle_d16.7102720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.28931590.23871436X-RAY DIFFRACTION86.87
1.97-1.990.25781630.21481467X-RAY DIFFRACTION91.93
1.99-2.020.22611680.20571511X-RAY DIFFRACTION91.8
2.02-2.040.22741670.19781493X-RAY DIFFRACTION92.43
2.04-2.070.22771710.20771536X-RAY DIFFRACTION93.08
2.07-2.10.25251700.20431534X-RAY DIFFRACTION92.46
2.1-2.130.25991610.20741462X-RAY DIFFRACTION89.57
2.13-2.160.24331700.18941512X-RAY DIFFRACTION92.27
2.16-2.190.22461710.19251554X-RAY DIFFRACTION94.11
2.19-2.230.22621700.18021522X-RAY DIFFRACTION94.74
2.23-2.270.22571740.16781561X-RAY DIFFRACTION95.38
2.27-2.310.22011720.16951556X-RAY DIFFRACTION94.68
2.31-2.350.22511710.1621540X-RAY DIFFRACTION94.84
2.35-2.40.19621740.16621567X-RAY DIFFRACTION95.19
2.4-2.450.2231710.17511527X-RAY DIFFRACTION94.75
2.46-2.510.21281690.16731532X-RAY DIFFRACTION91.16
2.51-2.570.19931740.16731551X-RAY DIFFRACTION96.15
2.57-2.640.19041760.16321585X-RAY DIFFRACTION96.18
2.64-2.720.21131720.15651556X-RAY DIFFRACTION95.95
2.72-2.810.1781790.15091607X-RAY DIFFRACTION96.33
2.81-2.910.19641750.14441579X-RAY DIFFRACTION96.8
2.91-3.030.18511760.14951578X-RAY DIFFRACTION96.48
3.03-3.160.16281700.1471530X-RAY DIFFRACTION91.99
3.16-3.330.1731800.14811620X-RAY DIFFRACTION98.09
3.33-3.540.16081760.12561598X-RAY DIFFRACTION97.58
3.54-3.810.14481790.13051608X-RAY DIFFRACTION97.97
3.81-4.20.18291810.1421630X-RAY DIFFRACTION97.89
4.2-4.80.15311740.12811554X-RAY DIFFRACTION94.53
4.8-6.050.18151820.16021644X-RAY DIFFRACTION98.54
6.05-40.080.21591810.20731642X-RAY DIFFRACTION96.15

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