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- PDB-4rbt: PduA K26A S40L mutant, from Salmonella enterica serovar Typhimuri... -

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Basic information

Entry
Database: PDB / ID: 4rbt
TitlePduA K26A S40L 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 subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 12, 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2994
Polymers31,2033
Non-polymers961
Water724
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)62,6949
Polymers62,4066
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9250 Å2
ΔGint-112 kcal/mol
Surface area19500 Å2
MethodPISA
2
C: Propanediol utilization protein PduA
x 6


Theoretical massNumber of molelcules
Total (without water)62,4066
Polymers62,4066
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area8980 Å2
ΔGint-79 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.820, 116.820, 64.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Propanediol utilization protein PduA


Mass: 10401.016 Da / Num. of mol.: 3 / Fragment: UNP residues 2-94 / Mutation: K26A, S40L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: PduA, STM2038 / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES sodium salt pH 6.5, 2.0M Ammonium sulfate, 5% w/v PEG 400, 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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→54.134 Å / Num. all: 11772 / Num. obs: 11772 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.92 Å2 / Rmerge(I) obs: 0.102 / Χ2: 0.983 / Net I/σ(I): 15.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.360.0141.084542801194.2
2.36-2.420.0141.545977831198.7
2.42-2.50.0142.327033814199.6
2.5-2.570.0143.058310789199.7
2.57-2.660.0143.9510601775199.9
2.66-2.750.0145.712065736199.5
2.75-2.850.0147.0511934723199.4
2.85-2.970.0148.0411145690199.3
2.97-3.10.01410.610055666199.1
3.1-3.250.01413.3810594640199.4
3.25-3.430.01417.8110008611199.3
3.43-3.640.01422.999140571199
3.64-3.890.01426.688240552199.1
3.89-4.20.01432.218504512199
4.2-4.60.01439.727676475197.5
4.6-5.140.01442.546503430198.9
5.14-5.940.01439.826317389197.7
5.94-7.270.01440.664962332197.4
7.27-10.290.01452.213989269197.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGK

3ngk


Resolution: 2.3→54.134 Å / Cor.coef. Fo:Fc: 0.9444 / Cor.coef. Fo:Fc free: 0.9288 / SU R Cruickshank DPI: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1178 10.01 %RANDOM
Rwork0.2289 ---
all0.2328 11771 --
obs0.2328 11771 98.58 %-
Displacement parametersBiso max: 164.73 Å2 / Biso mean: 80.26 Å2 / Biso min: 39.42 Å2
Baniso -1Baniso -2Baniso -3
1-6.2816 Å20 Å20 Å2
2--6.2816 Å20 Å2
3----12.5631 Å2
Refine analyzeLuzzati coordinate error obs: 0.624 Å
Refinement stepCycle: LAST / Resolution: 2.3→54.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 5 4 1747
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d608SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes263HARMONIC5
X-RAY DIFFRACTIONt_it1751HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion254SEMIHARMONIC5
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_contact1945SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1751HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2380HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion20.48
LS refinement shellResolution: 2.3→2.52 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3006 270 10.02 %
Rwork0.2356 2425 -
all0.242 2695 -
obs--98.58 %
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)
17.3289-1.56981.05155.864-1.39520.92910.00340.0225-0.92870.04880.18380.29530.093-0.0032-0.1873-0.56430.01850.0262-0.5702-0.00430.607947.293714.641817.0829
26.9110.75590.03947.9966-1.12760.12940.09680.0898-0.03720.17340.040.4591-0.01660.0144-0.1367-0.5310.00580.0726-0.56890.00280.607936.904432.855917.223
36.17210.9497-0.06976.11830.39200.07390.18620.28930.128-0.0854-0.33950.0813-0.06280.0116-0.37340.03780.041-0.38090.02020.582219.15589.62315.1227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 90
2X-RAY DIFFRACTION2{ B|* }B4 - 89
3X-RAY DIFFRACTION3{ C|* }C4 - 89

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