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- PDB-3pac: Crystal structure of PduT a trimeric bacterial microcompartment p... -

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Basic information

Entry
Database: PDB / ID: 3pac
TitleCrystal structure of PduT a trimeric bacterial microcompartment protein with 4Fe-4S cluster binding site
ComponentsShell protein
KeywordsELECTRON TRANSPORT / BMC Domain / Shell Protein
Function / homology
Function and homology information


Bacterial microcompartment shell protein PduT / 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
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsPang, A.H. / Warren, M.J. / Pickersgill, R.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site
Authors: Pang, A. / Warren, M.J. / Pickersgill, R.W.
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Shell protein


Theoretical massNumber of molelcules
Total (without water)21,2271
Polymers21,2271
Non-polymers00
Water68538
1
A: Shell protein

A: Shell protein

A: Shell protein


Theoretical massNumber of molelcules
Total (without water)63,6803
Polymers63,6803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4550 Å2
ΔGint-31 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.680, 67.680, 62.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Shell protein / PduT microcompartment shell protein


Mass: 21226.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: pduT / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1VB78
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M NaCl, 0.1M Bicine, 25% PEG 550, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.933
SYNCHROTRONDiamond I0421.141
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 30, 2009
ADSC QUANTUM 3152CCDJul 17, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Silicon 111SINGLE WAVELENGTHMx-ray1
2Silicon 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
21.1411
ReflectionResolution: 1.86→33.84 Å / Num. all: 13647 / Num. obs: 13647 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.095 / Net I/σ(I): 18.5
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1979 / Rsym value: 0.58 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→29.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.807 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1372 10.1 %RANDOM
Rwork0.19862 ---
obs0.20394 12258 99.96 %-
all-13647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.825 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.86→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 0 38 1355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9671819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.0792542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14815232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.685156
X-RAY DIFFRACTIONr_chiral_restr0.1370.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021954
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_it1.3811.5904
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39121452
X-RAY DIFFRACTIONr_scbond_it4.033436
X-RAY DIFFRACTIONr_scangle_it6.3234.5367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 98 -
Rwork0.275 901 -
obs-1979 100 %

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