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- PDB-4rbv: PduA K26A S40GSG mutant, from Salmonella enterica serovar Typhimu... -

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Basic information

Entry
Database: PDB / ID: 4rbv
TitlePduA K26A S40GSG mutant, from Salmonella enterica serovar Typhimurium LT2
ComponentsPropanediol utilization protein PduA
KeywordsSTRUCTURAL PROTEIN / Bacterial Microcompartment shell protein
Function / homology
Function and homology information


propanediol degradation polyhedral organelle / propanediol catabolic process
Similarity search - Function
BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits ...BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartment shell protein PduA
Similarity search - Component
Biological speciesSalmonella enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsChun, S. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Selective molecular transport through the protein shell of a bacterial microcompartment organelle.
Authors: Chowdhury, C. / Chun, S. / Pang, A. / Sawaya, M.R. / Sinha, S. / Yeates, T.O. / Bobik, T.A.
History
DepositionSep 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Feb 28, 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: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,71110
Polymers73,4237
Non-polymers2883
Water362
1
A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
hetero molecules

A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
hetero molecules

A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2229
Polymers62,9346
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9560 Å2
ΔGint-107 kcal/mol
Surface area20990 Å2
MethodPISA
2
C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
hetero molecules

C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
hetero molecules

C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2229
Polymers62,9346
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_555z,-x+1/2,-y+1/21
crystal symmetry operation48_555-y+1/2,-z+1/2,x1
Buried area10060 Å2
ΔGint-102 kcal/mol
Surface area18890 Å2
MethodPISA
3
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
hetero molecules

E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1268
Polymers62,9346
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area10290 Å2
ΔGint-97 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.800, 236.800, 236.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23

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Components

#1: Protein
Propanediol utilization protein PduA


Mass: 10489.039 Da / Num. of mol.: 7 / Mutation: K26A, S40GSG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: PduA / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: P0A1C7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium sulfate, 2.2M Ammonium sulfate, 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→19.531 Å / Num. all: 19474 / Num. obs: 19474 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 135.22 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.001 / Net I/σ(I): 11.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.1-3.180.6941.734180143998.8
3.18-3.270.522.414059139099.1
3.27-3.360.3833.214057139098.7
3.36-3.470.2744.473807133498.5
3.47-3.580.19863599130198.4
3.58-3.710.1626.673120123597.8
3.71-3.850.1378.343561120199.3
3.85-40.10910.513528117699.5
4-4.180.08213.143347112598.7
4.18-4.390.0714.973240109098.7
4.39-4.620.05617.72290699998.2
4.62-4.90.05418.05278096096.8
4.9-5.240.05418.05242488296.6
5.24-5.660.05217.44212081095.5
5.66-6.20.05717.69240278897.6
6.2-6.940.04620.54209269897.5
6.94-8.010.03425.97184261795.7
8.01-9.810.02930.39144550492.8
9.81-13.870.0328.84109139291.6
13.870.03230.1845214357

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.1→19.531 Å / Cor.coef. Fo:Fc: 0.9459 / Cor.coef. Fo:Fc free: 0.9314 / SU R Cruickshank DPI: 0.737 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1948 10 %RANDOM
Rwork0.1943 ---
all0.1967 19473 --
obs0.1967 19473 97.63 %-
Displacement parametersBiso max: 203.21 Å2 / Biso mean: 95.32 Å2 / Biso min: 46.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.663 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 15 2 4165
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1370SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes655HARMONIC5
X-RAY DIFFRACTIONt_it4194HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion618SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4904SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4194HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5728HARMONIC21.34
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion20.36
LS refinement shellResolution: 3.1→3.27 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3869 280 10.01 %
Rwork0.3532 2518 -
all0.3567 2798 -
obs--97.63 %
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)
13.4702-0.8673-1.36175.0011-1.61025.47710.1437-0.04930.14030.088-0.1049-0.0274-0.10590.2861-0.0388-0.10.0045-0.169-0.0525-0.012-0.037831.713257.826131.3306
26.8739-1.5191-2.0966.1723-2.453810.1187-0.1458-0.1165-0.13860.9977-0.0280.363-0.7168-0.68220.1739-0.0851-0.0398-0.012-0.20030.021-0.069821.630949.635649.1176
311.3608-1.5545-3.5127.50273.57846.5305-0.0703-0.1436-0.01020.0337-0.52710.7170.1088-1.00460.5974-0.19270.0995-0.1055-0.0303-0.0432-0.08999.631681.206935.3557
46.37891.8397-0.79655.7210.2914.16430.01050.4070.3563-0.4770.01690.1492-0.1294-0.5421-0.0275-0.08330.0547-0.1761-0.04420.0798-0.117518.718773.415417.8052
510.37822.7911-0.99934.4974-0.17785.42730.1497-0.7925-0.43330.43860.2668-0.14140.2331-0.7005-0.4165-0.1302-0.1261-0.14840.17490.1007-0.263-4.596850.414321.3241
612.0307-4.74934.52966.9369-0.819812.8260.11340.48430.01290.08140.034-0.13270.54510.9732-0.1474-0.32990.0337-0.11180.2715-0.2215-0.233620.287949.5647-6.4608
76.18860.05462.12940.58870.18299.2587-0.00530.2454-0.7356-0.05040.0439-0.0160.6484-0.1041-0.0386-0.0032-0.0719-0.1682-0.1322-0.0891-0.068415.518549.817514.7925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 95
2X-RAY DIFFRACTION2{ B|* }B1 - 94
3X-RAY DIFFRACTION3{ C|* }C3 - 91
4X-RAY DIFFRACTION4{ D|* }D4 - 92
5X-RAY DIFFRACTION5{ E|* }E4 - 92
6X-RAY DIFFRACTION6{ F|* }F5 - 94
7X-RAY DIFFRACTION7{ G|* }G3 - 91

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