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- PDB-4p2s: Alanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Ly... -

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Entry
Database: PDB / ID: 4p2s
TitleAlanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Lysine Triad Essential to Assembly of the Shell of the Pdu Microcompartment
ComponentsPutative propanediol utilization protein PduA
KeywordsBIOSYNTHETIC PROTEIN / Microcompartment / 1 / 2-propanediol / Carboxysome / B12
Function / homologyBMC (bacterial microcompartment) domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Saintpaul str. SARA26 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsSinha, S. / Cheng, S. / Sung, Y.W. / McNamara, D.E. / Sawaya, M.R. / Yeates, T.O. / Bobik, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthAI081146 United States
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Alanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Lysine Triad Essential to Assembly of the Shell of the Pdu Microcompartment.
Authors: Sinha, S. / Cheng, S. / Sung, Y.W. / McNamara, D.E. / Sawaya, M.R. / Yeates, T.O. / Bobik, T.A.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative propanediol utilization protein PduA
B: Putative propanediol utilization protein PduA
C: Putative propanediol utilization protein PduA
D: Putative propanediol utilization protein PduA
E: Putative propanediol utilization protein PduA
F: Putative propanediol utilization protein PduA
G: Putative propanediol utilization protein PduA
H: Putative propanediol utilization protein PduA
I: Putative propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80222
Polymers94,5559
Non-polymers1,24713
Water4,684260
1
A: Putative propanediol utilization protein PduA
B: Putative propanediol utilization protein PduA
C: Putative propanediol utilization protein PduA
D: Putative propanediol utilization protein PduA
E: Putative propanediol utilization protein PduA
F: Putative propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,91215
Polymers63,0376
Non-polymers8759
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-107 kcal/mol
Surface area20280 Å2
MethodPISA
2
G: Putative propanediol utilization protein PduA
H: Putative propanediol utilization protein PduA
I: Putative propanediol utilization protein PduA
hetero molecules

G: Putative propanediol utilization protein PduA
H: Putative propanediol utilization protein PduA
I: Putative propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,78114
Polymers63,0376
Non-polymers7458
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area12440 Å2
ΔGint-135 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.156, 105.402, 67.269
Angle α, β, γ (deg.)90.000, 94.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-101-

GOL

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Components

#1: Protein
Putative propanediol utilization protein PduA / PduA


Mass: 10506.132 Da / Num. of mol.: 9 / Mutation: K26A
Source method: isolated from a genetically manipulated source
Details: synthetic gene
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Saintpaul str. SARA26 (bacteria)
Gene: SES26_19178 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: V1FW89
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 4.02 Å3/Da / Density % sol: 69.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.2 M ammonium sulfate and 0.2 M potassium formate. Crystals took about 3-7 days to develop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.94→100 Å / Num. all: 89887 / Num. obs: 89887 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 34.07 Å2 / Rmerge(I) obs: 0.077 / Χ2: 0.952 / Net I/av σ(I): 15.69 / Net I/σ(I): 7.7 / Num. measured all: 372311
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.94-2.0140.52390410.93197.2
2.01-2.0940.3888710.90295.5
2.09-2.184.30.27391090.91297.9
2.18-2.34.10.21390810.97597.8
2.3-2.444.10.15290390.97997.3
2.44-2.634.20.11589001.03395.4
2.63-2.94.30.09191530.98498.3
2.9-3.324.10.07388870.91995.4
3.32-4.184.20.05690600.93296.6
4.18-1004.10.05387460.94592.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å67.03 Å
Translation3 Å67.03 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
PHASER2.5.1phasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGK

3ngk


Resolution: 1.94→67.03 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9413 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4519 5.03 %RANDOM
Rwork0.1937 ---
obs0.1944 89773 95.4 %-
Displacement parametersBiso max: 225.53 Å2 / Biso mean: 47.7 Å2 / Biso min: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1--3.5961 Å20 Å2-2.5529 Å2
2---1.8183 Å20 Å2
3---5.4144 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.94→67.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 81 260 5909
Biso mean--67.42 47.49 -
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2002SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes863HARMONIC5
X-RAY DIFFRACTIONt_it5786HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion814SEMIHARMONIC5
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_contact6959SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5786HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7850HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion16.2
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 287 4.9 %
Rwork0.2679 5572 -
all0.2683 5859 -
obs--95.4 %
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)
11.35131.43280.02413.2663-0.63571.81890.1193-0.0530.07290.0775-0.17870.4995-0.0804-0.17420.0594-0.065-0.002-0.011-0.0614-0.05220.018119.4508-11.682667.0813
22.56891.1106-0.6932.9033-1.54274.269-0.13280.3217-0.1488-0.22540.1870.08450.0638-0.5182-0.0542-0.0335-0.0424-0.0325-0.0299-0.0341-0.095124.247-1.718448.4899
31.24030.60461.59211.990.84927.7476-0.01130.0186-0.0175-0.431-0.0275-0.01630.0319-0.44590.03880.0031-0.04070.0094-0.0356-0.0208-0.1335.719116.766348.522
41.35651.6982-0.63913.4608-0.25971.9834-0.07150.02210.1837-0.23570.03310.1901-0.101-0.15020.0384-0.0538-0.0136-0.0155-0.0183-0.007-0.036541.463925.94266.78
52.0531.173-1.07213.2352-0.98454.15370.1955-0.15090.02010.43-0.2105-0.0077-0.3978-0.020.0150.0163-0.0805-0.0006-0.0339-0.0037-0.138835.066216.809285.6302
60.460.45380.55692.95712.9855.71060.0664-0.19610.01080.2302-0.36980.3355-0.1317-0.30520.3034-0.0024-0.0710.0292-0.0581-0.0444-0.064824.3881-1.968985.8077
72.76210.4275-2.00740.828-0.84765.8626-0.1179-0.5348-0.03470.10840.1326-0.05720.3093-0.0612-0.0147-0.1758-0.00430.01890.02890.0050.01625.3588-36.883285.5729
84.4243-0.04520.67740.2612-0.11651.6538-0.0393-0.2019-0.5463-0.01380.03570.08820.1662-0.04270.0037-0.1285-0.02070.015-0.0853-0.0330.112816.5166-36.236267.3761
96.6069-1.35630.68041.52540.38463.91910.08610.5138-0.1017-0.05310.0506-0.04730.22610.3883-0.1367-0.1998-0.0029-0.00660.0304-0.0513-0.01455.0373-36.613548.289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 91
2X-RAY DIFFRACTION2{ B|* }B4 - 92
3X-RAY DIFFRACTION3{ C|* }C4 - 90
4X-RAY DIFFRACTION4{ D|* }D3 - 90
5X-RAY DIFFRACTION5{ E|* }E4 - 90
6X-RAY DIFFRACTION6{ F|* }F3 - 91
7X-RAY DIFFRACTION7{ G|* }G4 - 92
8X-RAY DIFFRACTION8{ H|* }H2 - 90
9X-RAY DIFFRACTION9{ I|* }I4 - 91

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