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Basic information

Entry
Database: PDB / ID: 7mmx
TitleCutN from Type I Cut MCP
ComponentsPropanediol utilization protein PduA
KeywordsSTRUCTURAL PROTEIN / microcompartment / MCP / shell protein / Cut MCP / choline utilization
Function / homologybacterial microcompartment / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Propanediol utilization protein PduA
Function and homology information
Biological speciesStreptococcus intermedius SK54 = ATCC 27335 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsOchoa, J.M. / 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 1.1Oct 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: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,94310
Polymers61,5596
Non-polymers3844
Water3,081171
1
A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
hetero molecules

A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,13512
Polymers61,5596
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10930 Å2
ΔGint-149 kcal/mol
Surface area19340 Å2
MethodPISA
2
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
hetero molecules

D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7518
Polymers61,5596
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10650 Å2
ΔGint-136 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.500, 49.660, 92.410
Angle α, β, γ (deg.)90.000, 93.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-101-

SO4

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Components

#1: Protein
Propanediol utilization protein PduA


Mass: 10259.764 Da / Num. of mol.: 6 / Fragment: BMC domain, residues 1-92 / Mutation: K27D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius SK54 = ATCC 27335 (bacteria)
Gene: HMPREF1654_00408 / Plasmid: plasmid / Details (production host): pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E2J8H5
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 1.26 M Ammonium sulfate, 0.1 M HEPES/ Sodium hydroxide pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→92.2 Å / Num. obs: 38026 / % possible obs: 98.5 % / Redundancy: 6.574 % / Biso Wilson estimate: 30.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Χ2: 0.991 / Net I/σ(I): 14.97 / Num. measured all: 249994 / Scaling rejects: 189
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
1.9-1.954.8510.7092.2512085279824910.8430.79489
1.95-26.1330.523.6816315275526600.9460.56896.6
2-2.066.7760.4185.0818200269926860.9610.45399.5
2.06-2.126.760.3466.1217663262126130.9630.37599.7
2.12-2.196.5620.2946.9216588253525280.9680.3299.7
2.19-2.276.8620.2627.9616804245624490.9750.28499.7
2.27-2.366.890.2059.7316239237123570.9850.22299.4
2.36-2.456.6750.15811.6715079227722590.9910.17199.2
2.45-2.566.3260.1412.2113741220921720.9910.15398.3
2.56-2.697.0760.1214.9114584206420610.9950.12999.9
2.69-2.837.0420.1021713999199719880.9960.1199.5
2.83-36.8150.08319.2412785187818760.9960.0999.9
3-3.216.9280.06723.3712270178117710.9970.07399.4
3.21-3.476.5750.05827.2410947167116650.9970.06399.6
3.47-3.86.160.04829.99240152415000.9980.05398.4
3.8-4.257.0410.04236.099815139813940.9980.04699.7
4.25-4.916.8380.0436.658411123912300.9980.04499.3
4.91-6.016.8320.04235.387051103710320.9980.04599.5
6.01-8.56.2620.04236.0951728318260.9990.04699.4
8.5-92.26.4230.0437.3230064684680.9990.043100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å92.2 Å
Translation1.9 Å92.2 Å

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Processing

Software
NameVersionClassification
BUSTERrefinement
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AXJ

4axj


Resolution: 1.9→92.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 3803 10 %RANDOM
Rwork0.212 ---
obs0.2144 38026 98.4 %-
Displacement parametersBiso max: 77.9 Å2 / Biso mean: 33.41 Å2 / Biso min: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.6262 Å20 Å22.1379 Å2
2---6.5185 Å20 Å2
3---1.8922 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.9→92.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 20 171 3798
Biso mean--51.23 39.93 -
Num. residues----522
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1206SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes623HARMONIC5
X-RAY DIFFRACTIONt_it3653HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion521SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_utility_angle7HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3384SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3653HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4974HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion15.5
LS refinement shellResolution: 1.9→1.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3384 76 9.99 %
Rwork0.3258 685 -
all0.3272 761 -
obs--83.46 %
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)
12.10480.11340.30850.34180.38460.5985-0.02060.02480.02390.040.025-0.0084-0.01610.0378-0.00440.00490.0002-0.019-0.0292-0.0044-0.01713.900713.723921.4338
22.12950.14352.31210.16520.07243.10040.05830.05340.08330.0046-0.01090.0599-0.0398-0.0154-0.0473-0.03530.00260.0129-0.0130.0094-0.0441-16.404814.716313.6133
31.1502-0.314-0.76740.4707-0.04861.925-0.0587-0.1074-0.022-0.0350.05490.0199-0.06690.08970.0038-0.020.0114-0.0221-0.0192-0.0016-0.017-21.312214.3505-6.8089
42.4483-0.36120.92410.226-0.4981.7275-0.0417-0.12440.032-0.03580.04840.0187-0.0841-0.0727-0.0067-0.00320.0111-0.0147-0.0277-0.0033-0.0233-8.4448-11.115924.9374
52.8008-0.25371.10790.2113-0.27082.68940.089-0.15550.2126-0.0643-0.03310.02420.01090.223-0.0558-0.0563-0.00880.02160.0236-0.0276-0.064612.2402-10.403330.7646
62.02710.9306-0.18360.32850.03763.6942-0.09430.2886-0.14660.13320.11480.0066-0.05970.2723-0.0205-0.1053-0.0182-0.00910.1114-0.0313-0.08617.6657-10.974752.0077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 89
2X-RAY DIFFRACTION2{ B|* }B5 - 92
3X-RAY DIFFRACTION3{ C|* }C-3 - 89
4X-RAY DIFFRACTION4{ D|* }D4 - 89
5X-RAY DIFFRACTION5{ E|* }E4 - 90
6X-RAY DIFFRACTION6{ F|* }F5 - 89

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