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- PDB-4i61: Crystal structure of a trimeric bacterial microcompartment shell ... -

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Basic information

Entry
Database: PDB / ID: 4i61
TitleCrystal structure of a trimeric bacterial microcompartment shell protein PduB
ComponentsPropanediol utilization protein PduB
KeywordsSTRUCTURAL PROTEIN / BMC Domain / Shell Protein
Function / homology
Function and homology information


bacterial microcompartment / structural molecule activity
Similarity search - Function
Bacterial microcompartment shell protein PduB / Bacterial microcompartment shell protein, EutL/PduB type / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Propanediol utilization protein PduB
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsPang, A.H. / Pickersgill, R.W.
CitationJournal: To be Published
Title: Propionaldehyde does not bind to PduB
Authors: Pang, A.H. / Prentice, M.B. / Pickersgill, R.W.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Propanediol utilization protein PduB
B: Propanediol utilization protein PduB
C: Propanediol utilization protein PduB


Theoretical massNumber of molelcules
Total (without water)81,1553
Polymers81,1553
Non-polymers00
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-60 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.010, 119.550, 147.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

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Components

#1: Protein Propanediol utilization protein PduB


Mass: 27051.662 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: ATCC 55730 / SD2112 / Gene: HMPREF0538_20934, pduB / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F8DQ39
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 1.87 Å3/Da / Density % sol: 34.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 1.4 M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2012
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→59.77 Å / Num. obs: 74480 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 9.6 / Redundancy: 4.9 % / Biso Wilson estimate: 9.916 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.074 / Net I/σ(I): 0.102
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.2 / Num. unique all: 26795 / Rsym value: 0.393 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FAY

4fay


Resolution: 1.64→59.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.925 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20028 3749 5 %RANDOM
Rwork0.15279 ---
all0.15519 98878 --
obs0.15519 70684 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.795 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.64→59.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4989 0 0 780 5769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225195
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9677042
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28824.667210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54915853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8121529
X-RAY DIFFRACTIONr_chiral_restr0.150.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213971
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2441.53420
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9225458
X-RAY DIFFRACTIONr_scbond_it3.41831775
X-RAY DIFFRACTIONr_scangle_it5.5954.51584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 272 -
Rwork0.253 5185 -
obs-5185 99.69 %

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