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- PDB-4rbu: PduA K26A S40Q mutant, from Salmonella enterica serovar Typhimuri... -

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Basic information

Entry
Database: PDB / ID: 4rbu
TitlePduA K26A S40Q mutant, from Salmonella enterica serovar Typhimurium LT2
ComponentsPropanediol utilization protein PduA
KeywordsSTRUCTURAL PROTEIN / Bacterial Micrcompartment 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 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 1.3Sep 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
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
H: Propanediol utilization protein PduA
I: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,22414
Polymers93,7449
Non-polymers4805
Water46826
1
A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)63,26414
Polymers62,4966
Non-polymers7698
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area11640 Å2
ΔGint-188 kcal/mol
Surface area19640 Å2
MethodPISA
2
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
H: Propanediol utilization protein PduA
I: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5927
Polymers62,4966
Non-polymers961
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-158 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.630, 108.630, 336.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Propanediol utilization protein PduA


Mass: 10415.987 Da / Num. of mol.: 9 / Mutation: K26A, S40Q
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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.05 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 2M AmSO4, 0.1M Cacodylate buffer pH 6.5, 0.2M NaCl, 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: 0.9789
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.79→94.08 Å / Num. obs: 30282 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 80.35 Å2 / Rmerge(I) obs: 0.342 / Net I/σ(I): 11.04
Reflection shellResolution: 2.79→2.86 Å / Rmerge(I) obs: 0.023 / Mean I/σ(I) obs: 1.84 / % possible all: 95.2

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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: 2.79→94.08 Å / Cor.coef. Fo:Fc: 0.8892 / Cor.coef. Fo:Fc free: 0.8576 / SU R Cruickshank DPI: 0.523 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 3023 10 %RANDOM
Rwork0.2285 ---
obs0.2309 30231 99.93 %-
all-30231 --
Displacement parametersBiso mean: 60.71 Å2
Baniso -1Baniso -2Baniso -3
1-9.2065 Å20 Å20 Å2
2--9.2065 Å20 Å2
3----18.413 Å2
Refine analyzeLuzzati coordinate error obs: 0.462 Å
Refinement stepCycle: LAST / Resolution: 2.79→94.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 0 25 26 5487
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015501HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.277502HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1876SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes831HARMONIC5
X-RAY DIFFRACTIONt_it5501HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion21.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion799SEMIHARMONIC5
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_contact6416SEMIHARMONIC4
LS refinement shellResolution: 2.79→2.89 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3358 285 9.99 %
Rwork0.2726 2567 -
all0.2789 2852 -
obs--99.93 %
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)
11.99620.1419-0.63576.1242-0.26482.3087-0.03780.1188-0.26340.0308-0.1610.54360.3215-0.36390.1987-0.06460.0115-0.01370.0167-0.0049-0.217549.4838-21.3047-0.3371
2-1.4609-0.2949-1.03116.33961.52716.48180.05690.08220.16660.46350.02330.48180.4663-0.16-0.0802-0.0921-0.04380.01770.00690.0085-0.164850.0779-11.381518.6749
3-0.61292.17260.22756.9117-0.00987.2749-0.03820.1512-0.0002-0.29410.14110.24060.2298-0.4487-0.1028-0.14090.0345-0.0431-0.0202-0.0242-0.125350.0106-10.313-19.0496
44.1625-2.9427-0.97452.15921.44484.5158-0.05730.12620.5510.1517-0.047-0.2941-0.49040.33180.1043-0.0042-0.0694-0.0005-0.01910.022-0.221472.6419-27.25570.0789
55.5328-2.40521.33481.4509-0.69565.0239-0.4747-0.33240.12610.38830.509-0.5241-0.29150.1025-0.0343-0.06880.0583-0.06010.0482-0.0605-0.233881.4847-33.38118.3383
66.2751-2.9614-1.62823.1615-0.31237.10740.14890.26980.4734-0.2232-0.2374-0.2213-0.42610.08630.0884-0.1303-0.0409-0.0188-0.05330.018-0.196482.9704-32.8322-18.1583
76.8578-1.9216-1.25752.1291-0.58483.9945-0.1248-0.02230.67480.1435-0.0427-0.3979-0.43640.26510.1675-0.00370.0165-0.0416-0.1459-0.0476-0.1452110.1541-49.37980.346
83.5332-3.36170.30972.4967-0.53115.59220.20580.37720.51290.03540.00280.16390.28150.2867-0.2086-0.12590.00760.0087-0.02730.0281-0.1059100.6797-44.8526-18.2743
98.1213-2.9420.46065.83243.358710.5354-0.3096-0.58780.26220.76940.5321-0.53030.19030.2041-0.22250.05830.1733-0.1056-0.1453-0.003-0.330699.8513-43.721218.8609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|4 - A|90 }A4 - 90
2X-RAY DIFFRACTION2{ B|4 - B|90 }B4 - 90
3X-RAY DIFFRACTION3{ C|4 - C|91 }C4 - 91
4X-RAY DIFFRACTION4{ D|3 - D|91 }D3 - 91
5X-RAY DIFFRACTION5{ E|4 - E|92 }E4 - 92
6X-RAY DIFFRACTION6{ F|4 - F|92 }F4 - 92
7X-RAY DIFFRACTION7{ G|2 - G|90 }G2 - 90
8X-RAY DIFFRACTION8{ H|4 - H|90 }H4 - 90
9X-RAY DIFFRACTION9{ I|4 - I|90 }I4 - 90

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