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- PDB-3n79: PduT C38S Mutant from Salmonella enterica Typhimurium -

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Basic information

Entry
Database: PDB / ID: 3n79
TitlePduT C38S Mutant from Salmonella enterica Typhimurium
ComponentsPduT
KeywordsELECTRON TRANSPORT / FeS Cluster / BMC shell protein / Pdu / Carboxysome
Function / homology
Function and homology information


propanediol degradation polyhedral organelle / propanediol catabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Bacterial microcompartment shell protein PduT / BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits ...Bacterial microcompartment shell protein PduT / BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartment shell protein PduT
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsCrowley, C.S. / Cascio, D. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell.
Authors: Crowley, C.S. / Cascio, D. / Sawaya, M.R. / Kopstein, J.S. / Bobik, T.A. / Yeates, T.O.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PduT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3774
Polymers20,2221
Non-polymers1553
Water2,000111
1
A: PduT
hetero molecules

A: PduT
hetero molecules

A: PduT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,13112
Polymers60,6673
Non-polymers4649
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6040 Å2
ΔGint-138 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.680, 67.680, 61.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein PduT / Propanediol utilization protein


Mass: 20222.355 Da / Num. of mol.: 1 / Mutation: C38S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: pduT, STM2054 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XDM8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.3M LiSO4, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 25637 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.251 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.93
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.783.1204301896100
1.54-1.580.5784.2201821836100
1.58-1.630.4395.619746178999.9
1.63-1.680.356.9193011747100
1.68-1.730.2668.9188741704100
1.73-1.790.1912181631639100
1.79-1.860.14815.2176011579100
1.86-1.940.10620.8169121522100
1.94-2.020.07926.8161911454100
2.02-2.120.06134.4157271410100
2.12-2.240.05438.3147991331100
2.24-2.370.04742.1139531253100
2.37-2.540.04447.413091118199.9
2.54-2.740.04151.6122241104100
2.74-30.03756.4112121022100
3-3.350.03562.49920925100
3.35-3.870.03464.3847281399.6
3.87-4.740.0365.8720368498.1
4.74-6.710.02964.9551753398
6.71-33.840.03158.6183921568.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→20 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.2 / σ(F): 0.18 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1286 5.16 %
Rwork0.189 --
obs0.191 24922 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.175 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 80.88 Å2 / Biso mean: 24.438 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1--2.012 Å20 Å20 Å2
2---2.012 Å20 Å2
3---4.025 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 7 111 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061418
X-RAY DIFFRACTIONf_angle_d1.0251940
X-RAY DIFFRACTIONf_chiral_restr0.068238
X-RAY DIFFRACTIONf_plane_restr0.003249
X-RAY DIFFRACTIONf_dihedral_angle_d13.266533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.560.2911290.2552427255690
1.56-1.6310.2481470.2262507265493
1.631-1.7170.2711320.2082593272596
1.717-1.8250.2371480.22649279797
1.825-1.9660.2351420.1962658280099
1.966-2.1630.2371510.18727042855100
2.163-2.4760.2261450.18727142859100
2.476-3.1190.2081690.19126972866100
3.119-29.6670.1661230.1692687281096
Refinement TLS params.Method: refined / Origin x: 19.6806 Å / Origin y: 39.1018 Å / Origin z: 12.8509 Å
111213212223313233
T0.0661 Å20.0064 Å20.0078 Å2-0.1155 Å2-0.0099 Å2--0.0926 Å2
L0.5739 °2-0.7964 °20.2966 °2-1.5602 °2-0.412 °2--0.3062 °2
S-0.065 Å °-0.1122 Å °0.095 Å °-0.0014 Å °0.1205 Å °-0.1439 Å °-0.02 Å °-0.033 Å °-0.04 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 184
2X-RAY DIFFRACTION1allA1 - 306
3X-RAY DIFFRACTION1allA1 - 193
4X-RAY DIFFRACTION1allA1 - 194
5X-RAY DIFFRACTION1allA1 - 195

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