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

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Basic information

Entry
Database: PDB / ID: 4olp
TitleLigand-free structure of the GrpU microcompartment shell protein from Pectobacterium wasabiae
ComponentsGrpU microcompartment shell protein
KeywordsELECTRON TRANSPORT / bacterial microcompartment / glycyl-radical propanediol / BMC shell protein / iron-sulfur cluster
Function / homologyBMC (bacterial microcompartment) domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesPectobacterium wasabiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsWheatley, N.M. / Thompson, M.C. / Gidaniyan, S.D. / Sawaya, M.R. / Jorda, J. / 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 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: GrpU microcompartment shell protein
B: GrpU microcompartment shell protein
C: GrpU microcompartment shell protein
D: GrpU microcompartment shell protein


Theoretical massNumber of molelcules
Total (without water)48,4884
Polymers48,4884
Non-polymers00
Water724
1
A: GrpU microcompartment shell protein
B: GrpU microcompartment shell protein

A: GrpU microcompartment shell protein
B: GrpU microcompartment shell protein

A: GrpU microcompartment shell protein
B: GrpU microcompartment shell protein


Theoretical massNumber of molelcules
Total (without water)72,7326
Polymers72,7326
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 area10060 Å2
ΔGint-42 kcal/mol
Surface area23980 Å2
MethodPISA
2
C: GrpU microcompartment shell protein
D: GrpU microcompartment shell protein

C: GrpU microcompartment shell protein
D: GrpU microcompartment shell protein

C: GrpU microcompartment shell protein
D: GrpU microcompartment shell protein


Theoretical massNumber of molelcules
Total (without water)72,7326
Polymers72,7326
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9120 Å2
ΔGint-45 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.845, 117.845, 76.023
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 2 - 94 / Label seq-ID: 2 - 94

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
GrpU microcompartment shell protein


Mass: 12122.048 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium wasabiae (bacteria) / Strain: WPP163 / Gene: Pecwa_4094 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: D0KBF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium/potassium phosphate, 30% 2-methyl-2,4-pentanediol, pH 6.0, 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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 23, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.79→100 Å / Num. obs: 9715 / % possible obs: 99.5 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.087 / Χ2: 2.005 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.79-2.96.10.6029371.284197.5
2.9-3.0270.4869911.081199.9
3.02-3.156.70.3459741.046198.9
3.15-3.3290.2549591.1771100
3.32-3.5317.70.2489681.1751100
3.53-3.817.40.1469961.222199.9
3.8-4.1815.60.0999548.391199.6
4.18-4.7917.20.0739851.0971100
4.79-6.0316.30.079861.0911100
6.03-10015.60.0699651.021199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→60.97 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2933 / WRfactor Rwork: 0.2392 / FOM work R set: 0.7014 / SU B: 49.587 / SU ML: 0.422 / SU R Cruickshank DPI: 0.3454 / SU Rfree: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 468 4.8 %RANDOM
Rwork0.2154 ---
obs0.2178 9710 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.72 Å2 / Biso mean: 99.336 Å2 / Biso min: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.65 Å2-1.83 Å20 Å2
2---3.65 Å20 Å2
3---11.86 Å2
Refinement stepCycle: LAST / Resolution: 2.79→60.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 0 4 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192668
X-RAY DIFFRACTIONr_bond_other_d0.0070.022727
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9863592
X-RAY DIFFRACTIONr_angle_other_deg1.44636249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61122.936109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.28115502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7411526
X-RAY DIFFRACTIONr_chiral_restr0.0910.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212877
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02559
X-RAY DIFFRACTIONr_mcbond_it4.5067.1931338
X-RAY DIFFRACTIONr_mcbond_other4.5057.1931337
X-RAY DIFFRACTIONr_mcangle_it6.94710.7531655
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: INTERATOMIC DISTANCE / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A44700.16
12B44700.16
21A44980.15
22C44980.15
31A41640.17
32D41640.17
41B49430.17
42C49430.17
51B44890.16
52D44890.16
61C44240.16
62D44240.16
LS refinement shellResolution: 2.79→2.863 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 33 -
Rwork0.366 633 -
all-666 -
obs--95.69 %
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)
13.23263.19660.85144.68151.18270.3033-0.07090.02520.6335-0.0906-0.09820.5105-0.0305-0.03850.16910.19160.0044-0.130.2053-0.00430.222-17.451214.445719.5561
22.6136-1.3192-1.13845.34231.26850.7029-0.10020.1005-0.2709-0.2849-0.03680.1986-0.16060.01590.13710.3069-0.0958-0.05890.17060.12690.17183.890223.527520.0585
36.29051.8385-0.29271.48740.3870.25990.20570.11210.54760.3706-0.14130.12380.1363-0.0439-0.06430.2152-0.0179-0.01110.2741-0.08160.08896.625822.5933-22.4456
44.45471.89510.38280.83460.20570.2178-0.0076-0.13680.3030.01040.03290.08720.12580.1157-0.02530.21520.06650.08780.2841-0.11710.1726-16.012216.9113-21.4349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 94
2X-RAY DIFFRACTION2B2 - 94
3X-RAY DIFFRACTION3C2 - 94
4X-RAY DIFFRACTION4D2 - 94

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