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

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Basic information

Entry
Database: PDB / ID: 4fay
TitleCrystal structure of a trimeric bacterial microcompartment shell protein PduB with glycerol metabolites
ComponentsMicrocompartments protein
Keywordsglycerol-binding protein / BMC Domain / Shell Protein
Function / homology
Function and homology information


1,2-propanediol catabolic process / 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
ACETATE ION / Bacterial microcompartment shell protein PduB
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPang, A.H. / Prentice, M.B. / Pickersgill, R.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB.
Authors: Pang, A. / Liang, M. / Prentice, M.B. / Pickersgill, R.W.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Apr 3, 2024Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,78021
Polymers81,1553
Non-polymers1,62518
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-76 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.865, 120.864, 145.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Microcompartments protein


Mass: 27051.662 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: DSM 20016 / Gene: Lreu_1748, PduB / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5VMB3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 35.02 %
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 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2012
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.55→72.78 Å / Num. obs: 87436 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.3
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2 / Num. unique all: 12243 / % possible all: 96.2

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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: EtuB

Resolution: 1.56→72.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.043 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20188 4338 4.9 %RANDOM
Rwork0.17263 ---
obs0.174 83762 99.62 %-
all-84081 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.56→72.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 106 401 5487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225332
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.987202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65924.396207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59315868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4571531
X-RAY DIFFRACTIONr_chiral_restr0.1140.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214009
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_it1.1021.53453
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71825514
X-RAY DIFFRACTIONr_scbond_it2.97131879
X-RAY DIFFRACTIONr_scangle_it4.684.51688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.555→1.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 337 -
Rwork0.4 5793 -
obs--95.17 %

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