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- PDB-7mn4: CmcB E35G mutant from Type II Cut MCP -

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Basic information

Entry
Database: PDB / ID: 7mn4
TitleCmcB E35G 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
CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
BMC domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsOchoa, J.M. / Mijares, O. / 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
DepositionApr 30, 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


Theoretical massNumber of molelcules
Total (without water)62,9646
Polymers62,9646
Non-polymers00
Water3,387188
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 area10930 Å2
ΔGint-96 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.390, 62.720, 67.390
Angle α, β, γ (deg.)90.000, 119.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 through 4 and (name N...
21(chain B and ((resid 3 through 4 and (name N...
31(chain C and (resid 3 through 42 or resid 44...
41(chain D and ((resid 3 through 4 and (name N...
51(chain E and ((resid 3 through 4 and (name N...
61(chain F and ((resid 3 through 4 and (name N...

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
11ASPASPALAALA(chain A and ((resid 3 through 4 and (name N...AA3 - 410 - 11
12ASPASPILEILE(chain A and ((resid 3 through 4 and (name N...AA3 - 9210 - 99
13ASPASPILEILE(chain A and ((resid 3 through 4 and (name N...AA3 - 9210 - 99
14ASPASPILEILE(chain A and ((resid 3 through 4 and (name N...AA3 - 9210 - 99
15ASPASPILEILE(chain A and ((resid 3 through 4 and (name N...AA3 - 9210 - 99
21ASPASPALAALA(chain B and ((resid 3 through 4 and (name N...BB3 - 410 - 11
22ASPASPILEILE(chain B and ((resid 3 through 4 and (name N...BB3 - 9210 - 99
23ASPASPILEILE(chain B and ((resid 3 through 4 and (name N...BB3 - 9210 - 99
24ASPASPILEILE(chain B and ((resid 3 through 4 and (name N...BB3 - 9210 - 99
25ASPASPILEILE(chain B and ((resid 3 through 4 and (name N...BB3 - 9210 - 99
31ASPASPVALVAL(chain C and (resid 3 through 42 or resid 44...CC3 - 4210 - 49
32ALAALAPROPRO(chain C and (resid 3 through 42 or resid 44...CC44 - 7951 - 86
33ASPASPILEILE(chain C and (resid 3 through 42 or resid 44...CC82 - 8389 - 90
34LYSLYSILEILE(chain C and (resid 3 through 42 or resid 44...CC85 - 9292 - 99
41ASPASPALAALA(chain D and ((resid 3 through 4 and (name N...DD3 - 410 - 11
42ASPASPTHRTHR(chain D and ((resid 3 through 4 and (name N...DD3 - 9310 - 100
43ASPASPTHRTHR(chain D and ((resid 3 through 4 and (name N...DD3 - 9310 - 100
44ASPASPTHRTHR(chain D and ((resid 3 through 4 and (name N...DD3 - 9310 - 100
45ASPASPTHRTHR(chain D and ((resid 3 through 4 and (name N...DD3 - 9310 - 100
51ASPASPALAALA(chain E and ((resid 3 through 4 and (name N...EE3 - 410 - 11
52ASPASPILEILE(chain E and ((resid 3 through 4 and (name N...EE3 - 9210 - 99
53ASPASPILEILE(chain E and ((resid 3 through 4 and (name N...EE3 - 9210 - 99
54ASPASPILEILE(chain E and ((resid 3 through 4 and (name N...EE3 - 9210 - 99
55ASPASPILEILE(chain E and ((resid 3 through 4 and (name N...EE3 - 9210 - 99
61ASPASPALAALA(chain F and ((resid 3 through 4 and (name N...FF3 - 410 - 11
62ASPASPILEILE(chain F and ((resid 3 through 4 and (name N...FF3 - 9210 - 99
63ASPASPILEILE(chain F and ((resid 3 through 4 and (name N...FF3 - 9210 - 99
64ASPASPILEILE(chain F and ((resid 3 through 4 and (name N...FF3 - 9210 - 99
65ASPASPILEILE(chain F and ((resid 3 through 4 and (name N...FF3 - 9210 - 99

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Components

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


Mass: 10494.015 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_2 / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G9V6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium choloride, 0.1 M Sodium HEPES pH 7.5, 30% PEG 400

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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: 1.8→58.39 Å / Num. obs: 44058 / % possible obs: 96.4 % / Redundancy: 5.29 % / Biso Wilson estimate: 31.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.093 / Χ2: 1.082 / Net I/σ(I): 9.05 / Num. measured all: 233088 / Scaling rejects: 79
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
1.8-1.845.0630.5392.0715563340330740.950.59790.3
1.84-1.895.3880.4642.6116719321531030.9610.51296.5
1.89-1.955.380.4022.9916797323231220.9750.44496.6
1.95-2.015.3020.3123.6315948311430080.9830.34496.6
2.01-2.075.0160.2434.5414199293928310.9830.2796.3
2.07-2.155.5140.2185.315754294028570.9890.2497.2
2.15-2.235.4860.1856.3914862278327090.9910.20397.3
2.23-2.325.4050.1816.7114238271026340.9890.19997.2
2.32-2.425.2740.1527.413397260825400.9940.16897.4
2.42-2.545.050.116911803243523370.9940.12996
2.54-2.685.5140.10810.512699234923030.9950.11998
2.68-2.845.4240.111.3411883223821910.9960.1197.9
2.84-3.045.3310.08713.3111089211820800.9950.09698.2
3.04-3.285.0180.07715.239238195118410.9950.08694.4
3.28-3.595.420.06118.659588179617690.9980.06798.5
3.59-4.025.3410.05620.618802168416480.9980.06297.9
4.02-4.645.0520.04622.557027143213910.9980.05297.1
4.64-5.685.1530.04521.636075124111790.9980.0595
5.68-8.035.1880.04821.3647949509240.9980.05497.3
8.03-58.395.0540.03925.3226135655170.9990.04491.5

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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: 1.8→58.39 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 4380 10 %
Rwork0.2002 39441 -
obs0.2041 43821 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.99 Å2 / Biso mean: 31.7658 Å2 / Biso min: 19.73 Å2
Refinement stepCycle: final / Resolution: 1.8→58.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 0 188 3996
Biso mean---37.95 -
Num. residues----541
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2197X-RAY DIFFRACTION6.83TORSIONAL
12B2197X-RAY DIFFRACTION6.83TORSIONAL
13C2197X-RAY DIFFRACTION6.83TORSIONAL
14D2197X-RAY DIFFRACTION6.83TORSIONAL
15E2197X-RAY DIFFRACTION6.83TORSIONAL
16F2197X-RAY DIFFRACTION6.83TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.820.40221280.36821147127583
1.82-1.840.32271400.32731280142096
1.84-1.860.34151440.30081284142896
1.86-1.880.32811470.29061340148796
1.88-1.910.33361440.261283142796
1.91-1.930.29861420.25971289143196
1.93-1.960.31171470.26411331147896
1.96-1.990.32981410.23871287142896
1.99-2.020.25241430.23411283142696
2.02-2.060.27641500.22841345149595
2.06-2.090.26691460.22151304145096
2.09-2.130.28321450.20641296144197
2.13-2.170.26931480.21031329147796
2.17-2.210.25061440.20571285142998
2.22-2.260.23141500.19231347149797
2.26-2.320.23931490.20061351150097
2.32-2.370.30071450.21331315146098
2.37-2.440.24651450.19761324146997
2.44-2.510.2441450.18661295144094
2.51-2.590.25461500.19811343149398
2.59-2.680.21411470.19381315146299
2.68-2.790.24771510.19511368151998
2.79-2.920.23031480.22151330147898
2.92-3.070.26631520.19531368152098
3.07-3.260.24551400.21921253139394
3.26-3.520.20011500.19341362151299
3.52-3.870.22351500.18291351150199
3.87-4.430.18011520.16051362151498
4.43-5.580.21721450.15461324146995
5.58-58.390.21941520.1931350150295
Refinement TLS params.Method: refined / Origin x: 20.7666 Å / Origin y: -14.8311 Å / Origin z: 21.6779 Å
111213212223313233
T0.2503 Å2-0.0515 Å20.0162 Å2-0.218 Å2-0.0629 Å2--0.2518 Å2
L0.7634 °2-0.0468 °20.1141 °2-0.0245 °2-0.0446 °2--0.539 °2
S0.0185 Å °0.0301 Å °-0.0132 Å °-0.0016 Å °-0.0102 Å °0.0003 Å °0.0061 Å °0.0344 Å °-0.0103 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 92
2X-RAY DIFFRACTION1allB3 - 92
3X-RAY DIFFRACTION1allC3 - 92
4X-RAY DIFFRACTION1allD3 - 93
5X-RAY DIFFRACTION1allE3 - 92
6X-RAY DIFFRACTION1allF3 - 92
7X-RAY DIFFRACTION1allG1 - 198

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