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- PDB-7mpw: CmcB from Type II Cut MCP -

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Basic information

Entry
Database: PDB / ID: 7mpw
TitleCmcB 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
Bacterial microcompartment protein homohexamer
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / molecular replacement / Resolution: 3.001 Å
AuthorsOchoa, J.M. / Marshall, J.D. / 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 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)63,6616
Polymers63,6616
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, CmcB 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 area8190 Å2
ΔGint-72 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.230, 52.400, 61.160
Angle α, β, γ (deg.)107.420, 96.580, 101.960
Int Tables number1
Space group name H-MP1

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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: 10610.086 Da / Num. of mol.: 6 / Mutation: K25D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pduA_2 / Plasmid: pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G9V6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion
Details: 1.0 M Sodium acetate trihydrate, 0.1 M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→57.3 Å / Num. obs: 8055 / % possible obs: 97.1 % / Redundancy: 3.86 % / Biso Wilson estimate: 69.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.108 / Χ2: 0.882 / Net I/σ(I): 12.3 / Num. measured all: 31090 / Scaling rejects: 5
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
3-3.083.6830.6022.3221626495870.8490.70290.4
3.08-3.163.8940.5322.8321965795640.8740.61797.4
3.16-3.253.9170.3953.7422525965750.9250.45796.5
3.25-3.353.8920.3144.5921175625440.9580.36496.8
3.35-3.463.9020.2386.0119865275090.970.27696.6
3.46-3.593.890.178.0421165525440.9840.19798.6
3.59-3.723.8930.1459.1518925044860.990.16896.4
3.72-3.873.8990.1499.0518094754640.9890.17397.7
3.87-4.053.8930.11811.3318574904770.990.13797.3
4.05-4.243.8780.07215.2516254244190.9980.08498.8
4.24-4.473.8780.06219.2616564404270.9970.07197
4.47-4.743.8660.05820.8215314073960.9970.06897.3
4.74-5.073.8920.06319.4914093653620.9960.07399.2
5.07-5.483.810.06218.9513033483420.9960.07298.3
5.48-63.8620.09413.4812863373330.9930.10998.8
6-6.713.8660.06618.1811252962910.9960.07798.3
6.71-7.753.8310.04524.389962632600.9980.05298.9
7.75-9.493.7280.02735.958092202170.9990.03298.6
9.49-13.423.8220.02937.5964617116910.03498.8
13.42-57.33.5620.02737.0331791890.9990.03297.8

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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
BUSTERrefinement
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD
Starting model: 4QIV

4qiv


Resolution: 3.001→57.3 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.476
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 806 10.01 %RANDOM
Rwork0.2213 ---
obs0.2248 8055 97.4 %-
Displacement parametersBiso max: 127.03 Å2 / Biso mean: 70.1 Å2 / Biso min: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1--13.2045 Å2-14.1954 Å26.2587 Å2
2---1.3455 Å2-2.3848 Å2
3---14.55 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.001→57.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 0 7 3327
Biso mean---34.93 -
Num. residues----485
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1113SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes589HARMONIC5
X-RAY DIFFRACTIONt_it3331HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion484SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2575SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3331HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4534HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion16.21
LS refinement shellResolution: 3.001→3.03 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2535 21 10.4 %
Rwork0.3246 181 -
obs--84.68 %
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)
14.7622-2.6621.56945.265-2.307810.54110.07470.2237-0.0556-0.3174-0.1486-0.23960.08410.2680.0739-0.07280.0858-0.0728-0.0424-0.1255-0.19584.7642-24.72697.6328
23.2455-3.90461.07675.9299-0.47579.75950.024-0.0964-0.2634-0.1963-0.0771-0.1191-0.4435-0.45620.0531-0.05250.1125-0.0613-0.053-0.1196-0.1641-8.2983-11.18917.9082
31.6064-1.97371.60615.4533-0.72097.6389-0.1733-0.2039-0.18370.25520.0860.1583-0.7101-0.86540.08730.01060.19860.05330.0549-0.1046-0.2069-6.9569-9.589939.219
48.4487-4.44941.55535.38320.64946.4581-0.4932-0.50250.28220.35390.5938-0.032-0.0069-0.2341-0.1006-0.00850.12740.0253-0.0468-0.0178-0.28238.9455-21.455550.6318
53.1197-4.6113-0.03885.02941.906510.8395-0.1085-0.27220.36170.23110.14930.24430.71450.9298-0.0408-0.04010.1081-0.0055-0.01230.0243-0.217619.446-37.692240.8733
64.1817-2.29370.10932.1026-0.41518.8577-0.00090.1199-0.22960.1150.01760.18070.70730.5594-0.01670.01060.10280.0224-0.0536-0.1252-0.161117.3223-39.845218.7708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 86
2X-RAY DIFFRACTION2{ B|* }B3 - 83
3X-RAY DIFFRACTION3{ C|* }C3 - 81
4X-RAY DIFFRACTION4{ D|* }D3 - 83
5X-RAY DIFFRACTION5{ E|* }E3 - 81
6X-RAY DIFFRACTION6{ F|* }F4 - 84

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