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- PDB-4ppd: PduA K26A, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 4ppd
TitlePduA K26A, crystal form 2
ComponentsPropanediol utilization protein PduA
KeywordsSTRUCTURAL PROTEIN / BMC shell protein / Pdu / propanediol / mutagenesis / carboxysome
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: 2.4 Å
AuthorsMcNamara, D.E. / Sawaya, M.R. / Bobik, T.A. / Yeates, T.O.
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
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,48116
Polymers72,6257
Non-polymers8579
Water1,11762
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)63,10215
Polymers62,2506
Non-polymers8539
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11080 Å2
ΔGint-140 kcal/mol
Surface area21150 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)63,11415
Polymers62,2506
Non-polymers8659
Water1086
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 area10660 Å2
ΔGint-184 kcal/mol
Surface area19900 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)62,81812
Polymers62,2506
Non-polymers5686
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area10240 Å2
ΔGint-110 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.340, 235.340, 235.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11C-101-

SO4

21C-101-

SO4

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Components

#1: Protein
Propanediol utilization protein PduA


Mass: 10374.936 Da / Num. of mol.: 7 / Mutation: K26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: pduA, STM2038 / Plasmid: pTA925 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P0A1C7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.74 Å3/Da / Density % sol: 67.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 125 mM cesium sulfate, 1.8 M ammonium sulfate, pH 9.0, 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 / Detector: PIXEL / Date: Mar 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→83.205 Å / Num. all: 42127 / Num. obs: 42125 / % possible obs: 99.995 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.33 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.044 / Net I/σ(I): 32.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.4-2.461.0674.246386630923092100
2.46-2.530.8475.326118930633063100
2.53-2.60.7176.315711829142914100
2.6-2.680.5637.96153628672867100
2.68-2.770.4519.865878727552755100
2.77-2.870.35412.125611226662666100
2.87-2.980.26715.695364125832583100
2.98-3.10.21218.934938325012501100
3.1-3.240.15125.114739323752375100
3.24-3.390.10434.784907422832283100
3.39-3.580.07644.974590821632163100
3.58-3.80.06253.164305420722072100
3.8-4.060.05160.153788019291929100
4.06-4.380.04370.73627118101810100
4.38-4.80.03879.023507116611661100
4.8-5.370.03778.243133215251525100
5.37-6.20.03872.752478513291329100
6.2-7.590.03383.672376811421142100
7.59-10.730.02697.3317389881881100
10.73-83.2050.0388.74904551451499.6

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Phasing

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

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
PHENIXdev_1555refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NGK

3ngk


Resolution: 2.4→83.205 Å / FOM work R set: 0.8305 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 4213 10 %RANDOM
Rwork0.1947 ---
obs0.1972 42120 99.98 %-
all-42127 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.54 Å2 / Biso mean: 62.49 Å2 / Biso min: 28.99 Å2
Refinement stepCycle: LAST / Resolution: 2.4→83.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 47 62 4305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024266
X-RAY DIFFRACTIONf_angle_d0.585804
X-RAY DIFFRACTIONf_chiral_restr0.022747
X-RAY DIFFRACTIONf_plane_restr0.003738
X-RAY DIFFRACTIONf_dihedral_angle_d9.4331469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.4004-2.42770.2981380.2622124213801242
2.4277-2.45630.3511390.2538124713861247
2.4563-2.48620.31991450.2514131114561311
2.4862-2.51770.31411400.2464125213921252
2.5177-2.55080.27361370.2406124013771240
2.5508-2.58580.32441370.2485122813651228
2.5858-2.62270.28991400.2546126014001260
2.6227-2.66190.24931380.243123913771239
2.6619-2.70350.29011410.2396127614171276
2.7035-2.74780.27061400.2371125613961256
2.7478-2.79520.27781390.2415125513941255
2.7952-2.8460.28131390.2328124413831244
2.846-2.90070.26771400.2302126814081268
2.9007-2.960.2831410.2212126914101269
2.96-3.02430.23251420.2336127814201278
3.0243-3.09470.27181380.2341123613741236
3.0947-3.17210.26711400.2204125813981258
3.1721-3.25780.24491410.2175127214131272
3.2578-3.35370.23221380.2075124713851247
3.3537-3.4620.24761390.2043124613851246
3.462-3.58570.21481400.1985126414041264
3.5857-3.72930.22761420.1974127514171275
3.7293-3.8990.20211400.1824126014001260
3.899-4.10450.1891410.1754126714081267
4.1045-4.36170.17591420.1663128514271285
4.3617-4.69840.16371390.149124913881249
4.6984-5.17120.16681440.1596129114351291
5.1712-5.91930.21111410.1855126814091268
5.9193-7.4570.19261430.1868128814311288
7.457-83.25520.19991490.1703133614851336

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