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- PDB-7mpx: CmcC E36G mutant from Type II Cut MCP -

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Basic information

Entry
Database: PDB / ID: 7mpx
TitleCmcC E36G mutant from Type II Cut MCP
ComponentsBMC domain-containing protein
KeywordsSTRUCTURAL PROTEIN / microcompartment / MCP / shell protein / Cut MCP / choline utilization
Function / homology
Function and homology information


ethanolamine catabolic process / bacterial microcompartment
Similarity search - Function
Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Bacterial microcompartment protein homohexamer
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsOchoa, J.M. / Acosta, A.A. / Sawaya, M.R. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments
Authors: Ochoa, J.M. / Mijares, O. / Acosta, A.A. / Escoto, X. / Leon-Rivera, N. / Marshall, J.D. / Sawaya, M.R. / Yeates, T.O.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BMC domain-containing protein
B: BMC domain-containing protein
C: BMC domain-containing protein
D: BMC domain-containing protein
E: BMC domain-containing protein
F: BMC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1587
Polymers62,0636
Non-polymers951
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, CmcB E35G elutes as a hexamer. The elution profile is consistent with a predicted molecular mass of approximately 62 KDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-75 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.570, 61.000, 66.610
Angle α, β, γ (deg.)90.000, 119.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 77 or (resid 78...
21(chain B and (resid 3 through 64 or (resid 65...
31(chain C and (resid 3 through 64 or (resid 65...
41(chain D and (resid 3 through 77 or (resid 78...
51(chain E and (resid 3 through 64 or (resid 65...
61(chain F and (resid 3 through 64 or (resid 65...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALA(chain A and (resid 3 through 77 or (resid 78...AA3 - 7710 - 84
12ARGARGARGARG(chain A and (resid 3 through 77 or (resid 78...AA7885
13ARGARGASNASN(chain A and (resid 3 through 77 or (resid 78...AA2 - 819 - 88
14ARGARGASNASN(chain A and (resid 3 through 77 or (resid 78...AA2 - 819 - 88
15ARGARGASNASN(chain A and (resid 3 through 77 or (resid 78...AA2 - 819 - 88
16ARGARGASNASN(chain A and (resid 3 through 77 or (resid 78...AA2 - 819 - 88
17ARGARGASNASN(chain A and (resid 3 through 77 or (resid 78...AA2 - 819 - 88
18ARGARGASNASN(chain A and (resid 3 through 77 or (resid 78...AA2 - 819 - 88
21GLUGLUALAALA(chain B and (resid 3 through 64 or (resid 65...BB3 - 6410 - 71
22ARGARGARGARG(chain B and (resid 3 through 64 or (resid 65...BB6572
23GLUGLUASPASP(chain B and (resid 3 through 64 or (resid 65...BB3 - 8210 - 89
24GLUGLUASPASP(chain B and (resid 3 through 64 or (resid 65...BB3 - 8210 - 89
25GLUGLUASPASP(chain B and (resid 3 through 64 or (resid 65...BB3 - 8210 - 89
26GLUGLUASPASP(chain B and (resid 3 through 64 or (resid 65...BB3 - 8210 - 89
31GLUGLUALAALA(chain C and (resid 3 through 64 or (resid 65...CC3 - 6410 - 71
32ARGARGARGARG(chain C and (resid 3 through 64 or (resid 65...CC6572
33ARGARGASPASP(chain C and (resid 3 through 64 or (resid 65...CC2 - 829 - 89
41GLUGLUALAALA(chain D and (resid 3 through 77 or (resid 78...DD3 - 7710 - 84
42ARGARGARGARG(chain D and (resid 3 through 77 or (resid 78...DD7885
43ARGARGASPASP(chain D and (resid 3 through 77 or (resid 78...DD2 - 829 - 89
44ARGARGASPASP(chain D and (resid 3 through 77 or (resid 78...DD2 - 829 - 89
45ARGARGASPASP(chain D and (resid 3 through 77 or (resid 78...DD2 - 829 - 89
46ARGARGASPASP(chain D and (resid 3 through 77 or (resid 78...DD2 - 829 - 89
47ARGARGASPASP(chain D and (resid 3 through 77 or (resid 78...DD2 - 829 - 89
48ARGARGASPASP(chain D and (resid 3 through 77 or (resid 78...DD2 - 829 - 89
49ARGARGASPASP(chain D and (resid 3 through 77 or (resid 78...DD2 - 829 - 89
51GLUGLUALAALA(chain E and (resid 3 through 64 or (resid 65...EE3 - 6410 - 71
52ARGARGARGARG(chain E and (resid 3 through 64 or (resid 65...EE6572
53GLUGLUASPASP(chain E and (resid 3 through 64 or (resid 65...EE3 - 8210 - 89
54GLUGLUASPASP(chain E and (resid 3 through 64 or (resid 65...EE3 - 8210 - 89
55GLUGLUASPASP(chain E and (resid 3 through 64 or (resid 65...EE3 - 8210 - 89
61GLUGLUALAALA(chain F and (resid 3 through 64 or (resid 65...FF3 - 6410 - 71
62ARGARGARGARG(chain F and (resid 3 through 64 or (resid 65...FF6572
63ARGARGASNASN(chain F and (resid 3 through 64 or (resid 65...FF2 - 819 - 88

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Components

#1: Protein
BMC domain-containing protein / Propanediol utilization protein PduA / Putative propanediol utilization protein: polyhedral bodies ...Propanediol utilization protein PduA / Putative propanediol utilization protein: polyhedral bodies pduJ or pduA


Mass: 10343.847 Da / Num. of mol.: 6 / Mutation: K25A, E35G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pduA_3, pduA / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G9V7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 34.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M SPG buffer pH 6.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→57.73 Å / Num. obs: 26358 / % possible obs: 96.1 % / Redundancy: 5.108 % / Biso Wilson estimate: 47.538 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.118 / Χ2: 1.068 / Net I/σ(I): 6.83 / Num. measured all: 134627 / Scaling rejects: 2718
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.154.9681.430.879539201519200.731.59795.3
2.15-2.215.2581.1891.1510216195919430.81.32299.2
2.21-2.274.6560.6412.136067187013030.9080.73369.7
2.27-2.345.1660.8921.589288181917980.8340.99798.8
2.34-2.425.0410.5652.278999181217850.9590.63198.5
2.42-2.54.8170.4612.728242176417110.9630.51997
2.5-2.65.3860.3423.738870166616470.9850.37998.9
2.6-2.715.4540.2944.318819162816170.9860.32699.3
2.71-2.835.3790.2345.098467158715740.9910.2699.2
2.83-2.965.3380.1836.427841148014690.9920.20399.3
2.96-3.125.1320.1666.697118140813870.9950.18598.5
3.12-3.314.8690.1188.896446135313240.9950.13297.9
3.31-3.545.3460.09311.836730126612590.9940.10499.4
3.54-3.835.1320.07713.385732116911170.9960.08695.6
3.83-4.195.0640.06515.065393109910650.9980.07396.9
4.19-4.694.7920.05417.3845679779530.9980.0697.5
4.69-5.415.0060.05417.6542608738510.9980.06197.5
5.41-6.635.0990.0617.6438097557470.9970.06798.9
6.63-9.374.7190.04321.3726575875630.9980.04895.9
9.37-57.734.8220.04223.2915673353250.9990.04797

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å42.86 Å
Translation2 Å42.86 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000255588

Resolution: 2.1→57.73 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2832 2584 9.98 %RANDOM
Rwork0.2372 23297 --
obs0.2419 25881 94.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.8 Å2 / Biso mean: 61.6176 Å2 / Biso min: 43.82 Å2
Refinement stepCycle: final / Resolution: 2.1→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 5 47 3356
Biso mean--97.92 58.24 -
Num. residues----482
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2025X-RAY DIFFRACTION5.286TORSIONAL
12B2025X-RAY DIFFRACTION5.286TORSIONAL
13C2025X-RAY DIFFRACTION5.286TORSIONAL
14D2025X-RAY DIFFRACTION5.286TORSIONAL
15E2025X-RAY DIFFRACTION5.286TORSIONAL
16F2025X-RAY DIFFRACTION5.286TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.140.55511350.5211204133991
2.14-2.180.47271490.44961338148798
2.18-2.230.45421420.40761290143296
2.23-2.280.4658820.455876084256
2.28-2.340.4021500.36941342149299
2.34-2.40.43421480.34471339148798
2.4-2.470.39231460.31751302144896
2.47-2.550.4021460.30791310145696
2.55-2.640.32811460.27321304145098
2.64-2.750.32441530.25981373152699
2.75-2.870.33191460.25571320146699
2.87-3.020.27711480.24091384153298
3.02-3.210.31331450.25931299144496
3.21-3.460.23691470.20851337148498
3.46-3.810.3021440.20921304144896
3.81-4.360.23371520.17621366151898
4.36-5.490.20881510.18381353150497
5.5-57.730.21441540.19191372152697
Refinement TLS params.Method: refined / Origin x: 16.757 Å / Origin y: -16.4238 Å / Origin z: 17.318 Å
111213212223313233
T0.4935 Å20.0312 Å2-0.0021 Å2-0.4779 Å20.1098 Å2--0.4998 Å2
L0.8298 °20.0495 °20.0878 °2-0.0375 °20.0794 °2--0.5039 °2
S0.0078 Å °-0.0641 Å °-0.0882 Å °0.0084 Å °-0.0077 Å °0.0041 Å °0.1073 Å °-0.0603 Å °-0.0036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 81
2X-RAY DIFFRACTION1allB3 - 82
3X-RAY DIFFRACTION1allC2 - 82
4X-RAY DIFFRACTION1allD2 - 82
5X-RAY DIFFRACTION1allE3 - 82
6X-RAY DIFFRACTION1allF2 - 81
7X-RAY DIFFRACTION1allG1 - 51
8X-RAY DIFFRACTION1allH1

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