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- PDB-5cyu: Structure of the soluble domain of EccB1 from the Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 5cyu
TitleStructure of the soluble domain of EccB1 from the Mycobacterium smegmatis ESX-1 secretion system.
ComponentsConserved membrane protein
KeywordsMEMBRANE PROTEIN / virulence / protein secretion / mycobacteria / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


membrane => GO:0016020 / hydrolase activity / ATP binding / plasma membrane
Similarity search - Function
Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain / TTHA1013/TTHA0281-like / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system ESX-1, transport TM domain B / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ESX-1 secretion system ATPase EccB1
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.07 Å
AuthorsArbing, M.A. / Chan, S. / Kahng, S. / Kim, J. / Eisenberg, D.S. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)TBSGC R01 (A1068135) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)TBSGC P01 (AI095208) United States
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.
Authors: Wagner, J.M. / Chan, S. / Evans, T.J. / Kahng, S. / Kim, J. / Arbing, M.A. / Eisenberg, D. / Korotkov, K.V.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Data collection
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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: Conserved membrane protein


Theoretical massNumber of molelcules
Total (without water)42,9971
Polymers42,9971
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.410, 74.410, 280.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Conserved membrane protein / Uncharacterized protein


Mass: 42997.336 Da / Num. of mol.: 1 / Fragment: UNP residues 73-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0060, MSMEI_0061 / Plasmid: pMAPLe4 / Details (production host): pET28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QNJ0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol Reservoir solution: 14% PEG 8000, 200 mM NaCl, 100 mM PO4-Citrate pH 4.2 Cryoprotectant: reservoir solution with 20% propylene glycol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.07→64.44 Å / Num. obs: 8748 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 113.7 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.11 / Χ2: 1.15 / Net I/σ(I): 13.67 / Num. measured all: 72652
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.07-3.158.30.5092.2231.0146666616032.37491.2
3.15-3.240.7851.571.5957646686381.66395.5
3.24-3.330.8081.1272.2551426105831.19595.6
3.33-3.430.9240.7493.4550926235930.79595.2
3.43-3.550.9580.554.750126045780.58395.7
3.55-3.670.9630.4176.2645725775470.44394.8
3.67-3.810.9840.3077.7442765725430.32794.9
3.81-3.960.9920.21910.3744645375040.23293.9
3.96-4.140.9940.15813.7744195384990.16892.8
4.14-4.340.9950.12817.2740254964640.13693.5
4.34-4.580.9960.09220.1638014824490.09993.2
4.58-4.850.9960.08621.7433744574220.09392.3
4.85-5.190.9960.07723.7231624414080.08292.5
5.19-5.610.9970.07824.8933064193870.08392.4
5.61-6.140.9980.06626.6729043803470.0791.3
6.14-6.870.9970.06326.9225043523220.06891.5
6.87-7.930.9960.0530.3220733212860.05489.1
7.93-9.710.9990.04335.719042812410.04685.8
9.71-13.730.9990.03935.5614072322000.04286.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KK7

4kk7


Resolution: 3.07→64.44 Å / Cor.coef. Fo:Fc: 0.8848 / Cor.coef. Fo:Fc free: 0.8628 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.565
RfactorNum. reflection% reflectionSelection details
Rfree0.2974 805 10.12 %RANDOM
Rwork0.2407 ---
obs0.2464 7954 85.14 %-
Displacement parametersBiso max: 190.11 Å2 / Biso mean: 91.15 Å2 / Biso min: 24.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.8784 Å20 Å20 Å2
2---3.8784 Å20 Å2
3---7.7568 Å2
Refine analyzeLuzzati coordinate error obs: 0.86 Å
Refinement stepCycle: final / Resolution: 3.07→64.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 0 10 2660
Biso mean---42.64 -
Num. residues----378
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1401SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes791HARMONIC5
X-RAY DIFFRACTIONt_it5200HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion385SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5645SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5200HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9435HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion2.71
LS refinement shellResolution: 3.07→3.43 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3517 171 10.56 %
Rwork0.2623 1448 -
all0.2711 1619 -
obs--85.14 %
Refinement TLS params.Method: refined / Origin x: 8.6166 Å / Origin y: 53.8013 Å / Origin z: 140.191 Å
111213212223313233
T-0.309 Å2-0.2187 Å2-0.1573 Å2--0.0021 Å20.1831 Å2--0.0701 Å2
L1.6909 °20.4145 °2-1.6347 °2-1.7304 °2-0.9778 °2--6.626 °2
S0.315 Å °-0.0693 Å °-0.1195 Å °-0.5278 Å °0.3906 Å °0.0599 Å °0.6715 Å °-0.8692 Å °-0.7056 Å °
Refinement TLS groupSelection details: { A|* }

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