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- PDB-4olo: Ligand-free structure of the GrpU microcompartment shell protein ... -

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Basic information

Entry
Database: PDB / ID: 4olo
TitleLigand-free structure of the GrpU microcompartment shell protein from Clostridiales bacterium 1_7_47FAA
ComponentsBMC domain protein
KeywordsELECTRON TRANSPORT / bacterial microcompartment / glycyl-radical propanediol / BMC shell protein / iron-sulfur cluster
Function / homologyBMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / BMC domain protein
Function and homology information
Biological speciesClostridiales bacterium 1_7_47FAA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsThompson, M.C. / Ahmed, H. / McCarty, K.N. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Identification of a unique fe-s cluster binding site in a glycyl-radical type microcompartment shell protein.
Authors: Thompson, M.C. / Wheatley, N.M. / Jorda, J. / Sawaya, M.R. / Gidaniyan, S.D. / Ahmed, H. / Yang, Z. / McCarty, K.N. / Whitelegge, J.P. / Yeates, T.O.
History
DepositionJan 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: BMC domain protein
B: BMC domain protein
C: BMC domain protein
D: BMC domain protein


Theoretical massNumber of molelcules
Total (without water)47,5714
Polymers47,5714
Non-polymers00
Water1,44180
1
A: BMC domain protein
B: BMC domain protein

A: BMC domain protein
B: BMC domain protein

A: BMC domain protein
B: BMC domain protein


Theoretical massNumber of molelcules
Total (without water)71,3566
Polymers71,3566
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8660 Å2
ΔGint-62 kcal/mol
Surface area24600 Å2
MethodPISA
2
C: BMC domain protein
D: BMC domain protein

C: BMC domain protein
D: BMC domain protein

C: BMC domain protein
D: BMC domain protein


Theoretical massNumber of molelcules
Total (without water)71,3566
Polymers71,3566
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8990 Å2
ΔGint-60 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.100, 130.100, 130.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
BMC domain protein /


Mass: 11892.642 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridiales bacterium 1_7_47FAA (bacteria)
Gene: CBFG_00659 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: C5EE96
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.86 Å3/Da / Density % sol: 68.11 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate, 2.0M ammonium sulfate, pH 4.5, vapor diffusion, hanging drop, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→19.84 Å / Num. obs: 25255 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 80.94 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.55
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.571.067817189299.8
2.57-2.641.497664181499.8
2.64-2.711.937518178499.8
2.71-2.83.057192171899.9
2.8-2.893.916961167599.9
2.89-2.995.186667162499.9
2.99-3.17.396322158599.9
3.1-3.2311.035540150399.2
3.23-3.3714.735837143299.4
3.37-3.5417.945872137199.3
3.54-3.7322.915597132299.5
3.73-3.9529.695205123998.9
3.95-4.2335.774764116898.2
4.23-4.5642.684218106097.2
4.56-543.5368298996.3
5-5.5943.64385890696.4
5.59-6.4640.22322877195.2
6.46-7.9149.39271465092.1
7.91-11.1853.42194151691.7
11.1857.27100723671.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
PHENIXphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.84 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.9389 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 2523 9.99 %RANDOM
Rwork0.1901 ---
obs0.1931 25254 98.6 %-
Displacement parametersBiso max: 188.88 Å2 / Biso mean: 87.07 Å2 / Biso min: 54.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.379 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 0 80 2563
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1024SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes354HARMONIC5
X-RAY DIFFRACTIONt_it2546HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion374SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3048SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2546HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3411HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.69
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2717 286 9.92 %
Rwork0.2288 2598 -
all0.2329 2884 -
obs--98.6 %
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)
15.2326-4.46180.88548.4929-0.91182.83690.10110.42930.0446-0.48990.0399-0.0695-0.0817-0.0238-0.141-0.09080.0751-0.0085-0.0016-0.0078-0.166722.952319.6666-6.5466
25.5053-1.6403-0.22533.67550.09184.8647-0.1372-0.07460.0324-0.109-0.0150.14270.11420.22610.1522-0.1540.0174-0.1258-0.0730.0466-0.03134.097131.1681.2821
38.3191-3.0199-3.55454.77861.24583.22220.0559-0.01290.3886-0.2987-0.0439-0.1893-0.41070.1028-0.012-0.06960.04110.1528-0.17530.0972-0.02632.663445.060612.6128
43.6821-0.833-0.2455.1105-2.01683.3496-0.0289-0.2276-0.00140.18710.24490.0318-0.18870.0223-0.2161-0.1554-0.02780.133-0.00650.0495-0.061147.35926.660215.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 102
2X-RAY DIFFRACTION2{ B|* }B1 - 102
3X-RAY DIFFRACTION3{ C|* }C1 - 102
4X-RAY DIFFRACTION4{ D|* }D1 - 104

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