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- PDB-7mgp: CmcA from Type II Cut MCP -

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Basic information

Entry
Database: PDB / ID: 7mgp
TitleCmcA from Type II Cut MCP
ComponentsBMC domain-containing protein
KeywordsSTRUCTURAL PROTEIN / microcompartment / MCP / shell protein / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsOchoa, J.M. / Escoto, X. / 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 13, 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

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Assembly

Deposited unit
A: BMC domain-containing protein


Theoretical massNumber of molelcules
Total (without water)10,3111
Polymers10,3111
Non-polymers00
Water48627
1
A: BMC domain-containing protein
x 6


Theoretical massNumber of molelcules
Total (without water)61,8656
Polymers61,8656
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
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area9460 Å2
ΔGint-97 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.860, 68.860, 27.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

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


Mass: 10310.915 Da / Num. of mol.: 1 / Mutation: K25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pduA_1 / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G9V5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2.5 M Sodium chloride, 0.1 M Imidazole/ Hydrochloric acid pH 8.0

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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: 1.65→59.63 Å / Num. obs: 9272 / % possible obs: 100 % / Redundancy: 9.833 % / Biso Wilson estimate: 24.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.069 / Χ2: 1.024 / Net I/σ(I): 19.49 / Num. measured all: 91175 / Scaling rejects: 47
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
1.65-1.699.6320.6473.1465216776770.910.685100
1.69-1.749.6710.514.1464316656650.9460.54100
1.74-1.799.6190.4364.9461086356350.9660.462100
1.79-1.849.2820.2797.258946356350.990.296100
1.84-1.919.2320.2139.3754475905900.9940.225100
1.91-1.9710.3820.16811.9261775955950.9960.177100
1.97-2.0510.4540.13414.9258235575570.9970.141100
2.05-2.1310.2510.12217.557105575570.9950.129100
2.13-2.2210.0820.1119.4652635225220.9950.116100
2.22-2.339.7640.09721.648925015010.9970.103100
2.33-2.469.3510.08323.7545074824820.9960.088100
2.46-2.6110.4710.07428.1946704464460.9980.078100
2.61-2.7910.440.06932.5845524364360.9980.073100
2.79-3.0110.1860.06533.9440033933930.9970.068100
3.01-3.39.6580.05537.0635253663650.9980.05899.7
3.3-3.699.2730.0539.131623413410.9980.053100
3.69-4.2610.1990.04644.6130292982970.9990.04999.7
4.26-5.229.980.04444.2625452552550.9980.046100
5.22-7.388.8090.04539.8117972042040.9980.048100
7.38-59.639.4030.04445.0611191191190.9990.047100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å59.85 Å
Translation1.8 Å59.85 Å

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Processing

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

4qiv


Resolution: 1.65→59.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.103 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 928 10.01 %RANDOM
Rwork0.2119 ---
obs0.2141 9272 100 %-
Displacement parametersBiso max: 58.12 Å2 / Biso mean: 30.05 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1-5.4365 Å20 Å20 Å2
2--5.4365 Å20 Å2
3----10.8729 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.65→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms647 0 0 27 674
Biso mean---36.12 -
Num. residues----93
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d220SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes113HARMONIC5
X-RAY DIFFRACTIONt_it656HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion97SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle1HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact639SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d656HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg891HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion17.86
LS refinement shellResolution: 1.65→1.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 47
RfactorNum. reflection% reflection
Rfree0.3951 21 10.4 %
Rwork0.3203 181 -
all0.3273 202 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 18.6661 Å / Origin y: 11.7056 Å / Origin z: 13.5125 Å
111213212223313233
T-0.0494 Å2-0.0238 Å20.0029 Å2--0.0363 Å20.0088 Å2--0.0187 Å2
L0.386 °2-0.9273 °20.0539 °2-3.8007 °20.5542 °2--0.6593 °2
S-0.073 Å °0.0225 Å °-0.0269 Å °0.015 Å °-0.0157 Å °0.0833 Å °-0.0343 Å °0.0077 Å °0.0887 Å °
Refinement TLS groupSelection details: { A|* }

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