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- PDB-4i0x: Crystal structure of the Mycobacterum abscessus EsxEF (Mab_3112-M... -

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Basic information

Entry
Database: PDB / ID: 4i0x
TitleCrystal structure of the Mycobacterum abscessus EsxEF (Mab_3112-Mab_3113) complex
Components(ESAT-6-like protein ...) x 2
KeywordsStructural Genomics / Unknown Function / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / TB Structural Genomics Consortium / TBSGC / WXG100 / ESAT-6-like protein / Secreted
Function / homology
Function and homology information


ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / ESAT-6-like protein / ESAT-6-like protein
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.956 Å
AuthorsArbing, M.A. / Chan, S. / Lu, J. / Kuo, E. / Harris, L. / Eisenberg, D. / Integrated Center for Structure and Function Innovation (ISFI) / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Plos One / Year: 2013
Title: Heterologous expression of mycobacterial Esx complexes in Escherichia coli for structural studies is facilitated by the use of maltose binding protein fusions.
Authors: Arbing, M.A. / Chan, S. / Harris, L. / Kuo, E. / Zhou, T.T. / Ahn, C.J. / Nguyen, L. / He, Q. / Lu, J. / Menchavez, P.T. / Shin, A. / Holton, T. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionNov 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESAT-6-like protein MAB_3112
B: ESAT-6-like protein MAB_3113
C: ESAT-6-like protein MAB_3112
D: ESAT-6-like protein MAB_3113
E: ESAT-6-like protein MAB_3112
F: ESAT-6-like protein MAB_3113
G: ESAT-6-like protein MAB_3112
H: ESAT-6-like protein MAB_3113
I: ESAT-6-like protein MAB_3112
J: ESAT-6-like protein MAB_3113
K: ESAT-6-like protein MAB_3112
L: ESAT-6-like protein MAB_3113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,61115
Polymers127,34412
Non-polymers2663
Water6,071337
1
A: ESAT-6-like protein MAB_3112
B: ESAT-6-like protein MAB_3113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3984
Polymers21,2242
Non-polymers1742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-35 kcal/mol
Surface area8510 Å2
MethodPISA
2
C: ESAT-6-like protein MAB_3112
D: ESAT-6-like protein MAB_3113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3163
Polymers21,2242
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-43 kcal/mol
Surface area8480 Å2
MethodPISA
3
E: ESAT-6-like protein MAB_3112
F: ESAT-6-like protein MAB_3113


Theoretical massNumber of molelcules
Total (without water)21,2242
Polymers21,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-36 kcal/mol
Surface area8800 Å2
MethodPISA
4
G: ESAT-6-like protein MAB_3112
H: ESAT-6-like protein MAB_3113


Theoretical massNumber of molelcules
Total (without water)21,2242
Polymers21,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-34 kcal/mol
Surface area7860 Å2
MethodPISA
5
I: ESAT-6-like protein MAB_3112
J: ESAT-6-like protein MAB_3113


Theoretical massNumber of molelcules
Total (without water)21,2242
Polymers21,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-35 kcal/mol
Surface area8370 Å2
MethodPISA
6
K: ESAT-6-like protein MAB_3112
L: ESAT-6-like protein MAB_3113


Theoretical massNumber of molelcules
Total (without water)21,2242
Polymers21,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-33 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.600, 74.060, 84.420
Angle α, β, γ (deg.)114.57, 103.28, 95.52
Int Tables number1
Space group name H-MP1
DetailsChains C and D / Chains E and F / Chains G and H / Chains I and J / Chains K and L

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Components

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ESAT-6-like protein ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
ESAT-6-like protein MAB_3112


Mass: 9796.523 Da / Num. of mol.: 6 / Mutation: S35N, R49K, V87A
Source method: isolated from a genetically manipulated source
Details: Co-expressed with Mab_3113 from a single plasmid. / Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / Gene: MAB_3112 / Plasmid: pMAPLe4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1MD68
#2: Protein
ESAT-6-like protein MAB_3113


Mass: 11427.521 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Co-expressed with Mab_3112 from a single plasmid. / Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / Gene: MAB_3113 / Plasmid: pMAPLe4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1MD69

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Non-polymers , 4 types, 340 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: RESERVOIR: 0.1M tri-sodium citrate, pH5.6, 0.2M potassium sodium tartrate, 2M ammonium sulfate. PROTEIN CONCENTRATION: 11 MG/ML. PROTEIN BUFFER: 20 mM Tris, pH 8.0, 150mM NaCl, 10% Glycerol, ...Details: RESERVOIR: 0.1M tri-sodium citrate, pH5.6, 0.2M potassium sodium tartrate, 2M ammonium sulfate. PROTEIN CONCENTRATION: 11 MG/ML. PROTEIN BUFFER: 20 mM Tris, pH 8.0, 150mM NaCl, 10% Glycerol, 2 mM B-ME. CRYO: reservoir solution plus 25% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2011
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.956→19.995 Å / Num. all: 72126 / Num. obs: 67097 / % possible obs: 93 % / Redundancy: 1.959 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.69

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.956→19.995 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 6709 10 %
Rwork0.1593 --
obs0.1647 67097 93.37 %
all-72126 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.956→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 15 337 7396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127172
X-RAY DIFFRACTIONf_angle_d1.1569667
X-RAY DIFFRACTIONf_dihedral_angle_d15.1952498
X-RAY DIFFRACTIONf_chiral_restr0.0741025
X-RAY DIFFRACTIONf_plane_restr0.0051279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9563-1.97850.33332050.2661838X-RAY DIFFRACTION85
1.9785-2.00170.26842280.22872059X-RAY DIFFRACTION94
2.0017-2.02610.26552180.21281962X-RAY DIFFRACTION94
2.0261-2.05180.25582340.19762098X-RAY DIFFRACTION95
2.0518-2.07870.26622210.19111994X-RAY DIFFRACTION94
2.0787-2.10720.25742270.19112052X-RAY DIFFRACTION95
2.1072-2.13720.25442250.18472028X-RAY DIFFRACTION95
2.1372-2.16910.22842370.17262132X-RAY DIFFRACTION96
2.1691-2.2030.23282240.16592013X-RAY DIFFRACTION96
2.203-2.2390.25662270.17512045X-RAY DIFFRACTION95
2.239-2.27760.24772290.16972063X-RAY DIFFRACTION94
2.2776-2.31890.21182260.1562028X-RAY DIFFRACTION95
2.3189-2.36350.20722270.14932050X-RAY DIFFRACTION96
2.3635-2.41160.21332330.14872093X-RAY DIFFRACTION96
2.4116-2.4640.20372270.14182043X-RAY DIFFRACTION96
2.464-2.52120.19512300.14842069X-RAY DIFFRACTION96
2.5212-2.58410.22762230.14372010X-RAY DIFFRACTION95
2.5841-2.65380.2112360.14832120X-RAY DIFFRACTION95
2.6538-2.73170.20862250.14422024X-RAY DIFFRACTION95
2.7317-2.81970.21822290.14952064X-RAY DIFFRACTION95
2.8197-2.92020.21182250.1512022X-RAY DIFFRACTION95
2.9202-3.03670.20562240.14832014X-RAY DIFFRACTION93
3.0367-3.17440.20872250.15572030X-RAY DIFFRACTION93
3.1744-3.3410.19432190.15451975X-RAY DIFFRACTION92
3.341-3.54930.24162130.14731915X-RAY DIFFRACTION89
3.5493-3.82150.17842120.14051909X-RAY DIFFRACTION88
3.8215-4.20290.16552100.13491884X-RAY DIFFRACTION88
4.2029-4.80370.16292130.13851920X-RAY DIFFRACTION89
4.8037-6.02460.22262230.19092007X-RAY DIFFRACTION93
6.0246-19.99580.22292140.17621927X-RAY DIFFRACTION90
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)
11.5131-1.5434-1.60493.84623.19064.3491-0.0170.00110.1099-0.0070.1391-0.20010.16240.2233-0.14490.0656-0.009-0.01410.1240.01190.1352-11.02024.106628.1791
22.7057-2.7914-1.73254.26022.10732.2813-0.1365-0.0661-0.12340.26250.09730.11250.30470.0610.04880.1271-0.0063-0.0180.11840.02220.1069-15.7981-1.227434.1876
31.9518-2.6687-1.76624.59872.01552.4002-0.0226-0.09320.0419-0.05260.0645-0.1750.03970.1918-0.07770.08510.00260.00690.1002-0.00930.1208-38.543241.032529.198
43.0973-4.0838-1.60035.96612.651.4618-0.0561-0.0414-0.07130.19740.00270.26340.0722-0.03450.03550.14260.00850.03390.14890.0340.1147-43.322236.335836.1228
56.8245-0.74534.45660.6717-0.79834.01630.15030.2245-0.1638-0.1022-0.00740.04710.214-0.0051-0.13990.105-0.0088-0.00240.1371-0.01540.128210.601-1.31225.0463
64.7444-0.05572.15051.2506-0.3752.3525-0.0669-0.19270.36990.0575-0.00780.0009-0.0881-0.19680.05740.1360.01480.01470.171-0.01220.1349.5844.877412.3622
72.84522.4753-1.94663.5963-2.42224.25830.24990.15010.03470.3344-0.00220.0152-0.2517-0.1904-0.23630.14920.00260.00570.1034-0.00460.1469-32.775720.344255.7289
83.9323.6013-2.20747.0195-2.82372.2610.3035-0.2416-0.43870.2831-0.3634-0.3727-0.1360.17140.02870.202-0.0534-0.06840.1824-0.03320.1837-24.233821.906759.9445
95.7998-0.15973.46360.3670.05363.2815-0.14350.3371-0.1577-0.14070.1305-0.0253-0.18370.1045-0.02210.1633-0.04730.02140.1297-0.01050.099-19.704731.08526.1376
105.08790.44221.64441.15110.32852.0765-0.5265-0.160.4509-0.13910.16070.0792-0.598-0.19580.25390.26850.0061-0.05740.16920.01010.1169-21.054438.013411.8424
112.31712.7832-1.94245.475-44.0369-0.11010.19680.1364-0.04090.24050.1258-0.1501-0.1916-0.17220.12110.0042-0.00940.10620.00010.1134-4.9349-9.55451.0789
121.66921.8677-1.36435.0359-2.93022.2927-0.0317-0.12-0.10760.1682-0.0378-0.2746-0.10990.12260.07310.1557-0.0295-0.02110.1687-0.0090.09231.7714-11.580856.8814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:76)
2X-RAY DIFFRACTION2(chain B and resid 8:90)
3X-RAY DIFFRACTION3(chain C and resid 2:76)
4X-RAY DIFFRACTION4(chain D and resid 9:91)
5X-RAY DIFFRACTION5(chain E and resid 3:69)
6X-RAY DIFFRACTION6(chain F and resid 7:96)
7X-RAY DIFFRACTION7(chain G and resid 2:69)
8X-RAY DIFFRACTION8(chain H and resid 12:87)
9X-RAY DIFFRACTION9(chain I and resid 1:76)
10X-RAY DIFFRACTION10(chain J and resid 10:88)
11X-RAY DIFFRACTION11(chain K and resid 2:78)
12X-RAY DIFFRACTION12(chain L and resid 9:90)

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