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- PDB-5d6v: PduJ K25A mutant, from Salmonella enterica serovar Typhimurium LT... -

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Basic information

Entry
Database: PDB / ID: 5d6v
TitlePduJ K25A mutant, from Salmonella enterica serovar Typhimurium LT2, PduJ mutant
ComponentsCarboxysome shell protein
KeywordsSTRUCTURAL PROTEIN / Bacterial Microcompartment shell protein
Function / homologybacterial microcompartment / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Propanediol utilization protein / Carboxysome structural protein EutM
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsBacterial Microcompartment shell protein
AuthorsChun, S. / Sawaya, M.R. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008496 United States
CitationJournal: Mol.Microbiol. / Year: 2016
Title: The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene.
Authors: Chowdhury, C. / Chun, S. / Sawaya, M.R. / Yeates, T.O. / Bobik, T.A.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxysome shell protein


Theoretical massNumber of molelcules
Total (without water)9,8481
Polymers9,8481
Non-polymers00
Water59433
1
A: Carboxysome shell protein
x 6


Theoretical massNumber of molelcules
Total (without water)59,0906
Polymers59,0906
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 area10170 Å2
ΔGint-88 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.870, 67.870, 26.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-132-

HOH

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Components

#1: Protein Carboxysome shell protein / Propanediol utilization protein PduJ


Mass: 9848.266 Da / Num. of mol.: 1 / Mutation: K25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: pduJ / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: Q7BV81, UniProt: H9L478*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.79 Å3/Da / Density % sol: 31.2 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→58.78 Å / Num. obs: 11398 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 18.61 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Χ2: 0.991 / Net I/σ(I): 18.08 / Num. measured all: 104768
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.545.50.8750.5642.7945298338290.62599.5
1.54-1.580.9320.5043.756668228220.546100
1.58-1.630.9580.4734.772917847840.501100
1.63-1.680.9640.3816.0676457637630.401100
1.68-1.730.9810.3217.0774507477470.339100
1.73-1.790.9870.2388.9669877227220.252100
1.79-1.860.9910.18811.0166286926920.199100
1.86-1.940.9960.13814.0767986696680.14699.9
1.94-2.020.9960.1216.3765186486480.126100
2.02-2.120.9970.0920.759616136130.096100
2.12-2.240.9980.08222.9254775905900.087100
2.24-2.370.9980.07326.3557415635630.076100
2.37-2.540.9980.06229.3651975235220.06599.8
2.54-2.740.9990.05831.747194894890.062100
2.74-30.9990.04934.8341984554550.052100
3-3.350.9990.04639.8940884124120.049100
3.35-3.870.9990.04243.6534763683680.044100
3.87-4.740.9990.03745.2827833113110.04100
4.74-6.710.9990.03747.6624092532530.039100
6.710.9980.03645.112071471470.038100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.29 Å58.87 Å
Translation3.29 Å58.87 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→58.78 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9165 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1140 10 %RANDOM
Rwork0.1908 ---
obs0.1935 11398 99.94 %-
Displacement parametersBiso max: 82.15 Å2 / Biso mean: 21.89 Å2 / Biso min: 11.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.3537 Å20 Å20 Å2
2--2.3537 Å20 Å2
3----4.7074 Å2
Refine analyzeLuzzati coordinate error obs: 0.174 Å
Refinement stepCycle: final / Resolution: 1.5→58.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms620 0 0 33 653
Biso mean---27.14 -
Num. residues----90
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d221SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes13HARMONIC2
X-RAY DIFFRACTIONt_gen_planes98HARMONIC5
X-RAY DIFFRACTIONt_it633HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion88SEMIHARMONIC5
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_contact790SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d633HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg863HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion15.12
LS refinement shellResolution: 1.5→1.64 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2294 268 9.99 %
Rwork0.18 2414 -
all0.1849 2682 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -1.7034 Å / Origin y: 21.9131 Å / Origin z: 12.7925 Å
111213212223313233
T-0.029 Å2-0.0058 Å20.0019 Å2--0.0525 Å20.0041 Å2--0.0288 Å2
L2.4209 °20.4732 °2-0.3317 °2-0.693 °2-0.202 °2--0.5437 °2
S-0.0034 Å °0.0036 Å °-0.0549 Å °-0.0155 Å °-0.0306 Å °-0.0286 Å °0.0198 Å °0.0149 Å °0.0339 Å °
Refinement TLS groupSelection details: { A|* }

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