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- PDB-3cgi: Crystal structure of the PduU shell protein from the Pdu microcom... -

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Basic information

Entry
Database: PDB / ID: 3cgi
TitleCrystal structure of the PduU shell protein from the Pdu microcompartment
ComponentsPropanediol utilization protein pduU
KeywordsUNKNOWN FUNCTION / circular permutation / beta barrel / bacterial microcompartment / propanediol / SIGNALING PROTEIN
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment shell protein EutS/PduU/CutR / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Propanediol utilization protein PduU
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCrowley, C.S. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Structure / Year: 2008
Title: Structure of the PduU Shell Protein from the Pdu Microcompartment of Salmonella
Authors: Crowley, C.S. / Sawaya, M.R. / Bobik, T.A. / Yeates, T.O.
History
DepositionMar 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: Propanediol utilization protein pduU
B: Propanediol utilization protein pduU
C: Propanediol utilization protein pduU
D: Propanediol utilization protein pduU


Theoretical massNumber of molelcules
Total (without water)54,2384
Polymers54,2384
Non-polymers00
Water2,972165
1
A: Propanediol utilization protein pduU
B: Propanediol utilization protein pduU

A: Propanediol utilization protein pduU
B: Propanediol utilization protein pduU

A: Propanediol utilization protein pduU
B: Propanediol utilization protein pduU


Theoretical massNumber of molelcules
Total (without water)81,3586
Polymers81,3586
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
Buried area17820 Å2
ΔGint-113.4 kcal/mol
Surface area24890 Å2
MethodPISA
2
C: Propanediol utilization protein pduU
D: Propanediol utilization protein pduU

C: Propanediol utilization protein pduU
D: Propanediol utilization protein pduU

C: Propanediol utilization protein pduU
D: Propanediol utilization protein pduU


Theoretical massNumber of molelcules
Total (without water)81,3586
Polymers81,3586
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
Buried area19090 Å2
ΔGint-115.9 kcal/mol
Surface area28100 Å2
MethodPISA
3
A: Propanediol utilization protein pduU
B: Propanediol utilization protein pduU
C: Propanediol utilization protein pduU
D: Propanediol utilization protein pduU

A: Propanediol utilization protein pduU
B: Propanediol utilization protein pduU
C: Propanediol utilization protein pduU
D: Propanediol utilization protein pduU

A: Propanediol utilization protein pduU
B: Propanediol utilization protein pduU
C: Propanediol utilization protein pduU
D: Propanediol utilization protein pduU


Theoretical massNumber of molelcules
Total (without water)162,71512
Polymers162,71512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area40850 Å2
ΔGint-227.4 kcal/mol
Surface area49060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.140, 74.140, 218.021
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

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Components

#1: Protein
Propanediol utilization protein pduU


Mass: 13559.595 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: pduU / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A1D1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM HEPES, 300 mM LiSO4, 20% PEG-3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2007
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. obs: 40948 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.159 / Χ2: 1.252 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.80.50538591.066193.5
1.86-1.944.30.42740671.17198.6
1.94-2.034.80.35941111.312199.8
2.03-2.135.10.31241361.421100
2.13-2.275.30.27441261.2271100
2.27-2.445.40.22441261.2261100
2.44-2.695.40.19541361.2731100
2.69-3.085.40.16241191.3131100
3.08-3.885.30.13241381.2121100
3.88-905.20.12441301.2211100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å72.68 Å
Translation4 Å72.68 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EWH

2ewh


Resolution: 1.8→61.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.761 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. Residue Asp41 from chains A, B, C, and D have an unusual torsion angles due to crystallographic packing.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2063 5 %RANDOM
Rwork0.203 ---
obs0.205 40944 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.646 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å2-1.27 Å20 Å2
2---2.55 Å20 Å2
3---3.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.137 Å0.146 Å
Refinement stepCycle: LAST / Resolution: 1.8→61.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 165 3623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223583
X-RAY DIFFRACTIONr_bond_other_d0.0010.022343
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.974873
X-RAY DIFFRACTIONr_angle_other_deg0.90535807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4135478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2724.815135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85815646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0751517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
X-RAY DIFFRACTIONr_nbd_refined0.1970.2668
X-RAY DIFFRACTIONr_nbd_other0.1830.22296
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21753
X-RAY DIFFRACTIONr_nbtor_other0.0860.21897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.218
X-RAY DIFFRACTIONr_mcbond_it2.65723039
X-RAY DIFFRACTIONr_mcbond_other0.7142951
X-RAY DIFFRACTIONr_mcangle_it3.01233756
X-RAY DIFFRACTIONr_scbond_it2.43321409
X-RAY DIFFRACTIONr_scangle_it3.33431107
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 141 -
Rwork0.292 2638 -
all-2779 -
obs--91.38 %
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)
10.7358-0.0594-0.56750.2339-0.16970.70530.0048-0.03010.01380.0279-0.0245-0.0508-0.01460.05280.0197-0.02510.0069-0.0067-0.0019-0.009-0.021219.94591.259715.2468
20.92750.418-0.20170.5347-0.44280.5719-0.0041-0.01820.16230.02270.00960.0206-0.01170.0154-0.0056-0.0123-0.0071-0.0016-0.0213-0.0058-0.0258.91317.942115.2975
30.41570.0660.19250.92240.26570.62970.02810.01220.0257-0.064-0.0255-0.1989-0.05780.0088-0.0026-0.0076-0.01910.0059-0.01090.011-0.046715.890611.4877-22.8582
41.1130.03260.4010.3145-0.05410.67310.02360.0284-0.11-0.0356-0.0159-0.10210.0450.0624-0.0077-0.01240.00320.01420.020.0124-0.076918.3615-8.4882-22.3922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1187 - 118
2X-RAY DIFFRACTION2BB7 - 1187 - 118
3X-RAY DIFFRACTION3CC4 - 1224 - 122
4X-RAY DIFFRACTION4DD6 - 1226 - 122

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