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- PDB-3q4h: Crystal structure of the Mycobacterium smegmatis EsxGH complex (M... -

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Basic information

Entry
Database: PDB / ID: 3q4h
TitleCrystal structure of the Mycobacterium smegmatis EsxGH complex (MSMEG_0620-MSMEG_0621)
Components
  • Low molecular weight protein antigen 7
  • Pe family protein
KeywordsMETAL TRANSPORT / Structural Genomics / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / TB Structural Genomics Consortium / TBSGC / 4-helix bundle / WXG100 motif / ESAT-6/ CFP-10 family / UNKNOWN FUNCTION
Function / homology
Function and homology information


extracellular region
Similarity search - Function
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
ESAT-6-like protein EsxG / ESAT-6-like protein EsxH
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsChan, S. / Harris, L. / Kuo, E. / Ahn, C. / Zhou, T.T. / Nguyen, L. / Shin, A. / Sawaya, M.R. / Cascio, D. / Arbing, M.A. ...Chan, S. / Harris, L. / Kuo, E. / Ahn, C. / Zhou, T.T. / Nguyen, L. / Shin, A. / Sawaya, M.R. / Cascio, D. / Arbing, M.A. / 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
DepositionDec 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3May 14, 2014Group: Database references
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pe family protein
B: Low molecular weight protein antigen 7
C: Pe family protein
D: Low molecular weight protein antigen 7


Theoretical massNumber of molelcules
Total (without water)44,1034
Polymers44,1034
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-84 kcal/mol
Surface area15440 Å2
MethodPISA
2
A: Pe family protein
B: Low molecular weight protein antigen 7

C: Pe family protein
D: Low molecular weight protein antigen 7


Theoretical massNumber of molelcules
Total (without water)44,1034
Polymers44,1034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z+1/21
Buried area7950 Å2
ΔGint-82 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.598, 105.598, 71.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEARGARG3AA8 - 269 - 27
211ILEILEARGARG3CC8 - 269 - 27
121SERSERALAALA3AA27 - 3628 - 37
221SERSERALAALA3CC27 - 3628 - 37
131PHEPHEVALVAL5AA51 - 6152 - 62
231PHEPHEVALVAL5CC51 - 6152 - 62
141SERSERSERSER2AA62 - 8263 - 83
241SERSERSERSER2CC62 - 8263 - 83
151TYRTYRALAALA5AA83 - 9084 - 91
251TYRTYRALAALA5CC83 - 9084 - 91
112MSEMSEGLUGLU5BB11 - 1711 - 17
212MSEMSEGLUGLU5DD11 - 1711 - 17
122MSEMSEALAALA5BB18 - 2418 - 24
222MSEMSEALAALA5DD18 - 2418 - 24
132LEULEULEULEU3BB25 - 3925 - 39
232LEULEULEULEU3DD25 - 3925 - 39
142ALAALAGLNGLN5BB40 - 4440 - 44
242ALAALAGLNGLN5DD40 - 4440 - 44
152MSEMSEGLNGLN3BB49 - 5549 - 55
252MSEMSEGLNGLN3DD49 - 5549 - 55
162ALAALALEULEU2BB56 - 6556 - 65
262ALAALALEULEU2DD56 - 6556 - 65
172VALVALTHRTHR5BB66 - 7466 - 74
272VALVALTHRTHR5DD66 - 7466 - 74
182HISHISALAALA6BB76 - 8276 - 82
282HISHISALAALA6DD76 - 8276 - 82

NCS ensembles :
ID
1
2

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Components

#1: Protein Pe family protein


Mass: 10221.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_0620 / Plasmid: pMAPLe3, pET28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: A0QQ43
#2: Protein Low molecular weight protein antigen 7


Mass: 11829.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_0621 / Plasmid: pMAPLe3, pET28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: A0QQ44
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 460mM K-Na-Tartrate, 35% Glycerol, 95mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.7→80 Å / Num. all: 12416 / Num. obs: 46063 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Redundancy: 3.7 % / Rsym value: 0.099 / Net I/σ(I): 8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1231 / Rsym value: 0.482 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→80 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.867 / SU B: 23.617 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.661 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 636 5.1 %RANDOM
Rwork0.20737 ---
obs0.21022 11779 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.436 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.89 Å20 Å2
2--1.79 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.7→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 0 33 2480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212491
X-RAY DIFFRACTIONr_bond_other_d0.0010.021484
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.8913389
X-RAY DIFFRACTIONr_angle_other_deg0.82233628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8635336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68325108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6115343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.258158
X-RAY DIFFRACTIONr_chiral_restr0.0470.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.51686
X-RAY DIFFRACTIONr_mcbond_other0.0521.5686
X-RAY DIFFRACTIONr_mcangle_it0.89422605
X-RAY DIFFRACTIONr_scbond_it1.6813805
X-RAY DIFFRACTIONr_scangle_it2.5234.5784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A297tight positional0.110.05
22B191tight positional0.110.05
11A206medium positional0.140.5
22B228medium positional0.360.5
11A293loose positional0.615
22B375loose positional0.75
11A297tight thermal0.210.5
22B191tight thermal0.680.5
11A206medium thermal0.222
22B228medium thermal1.062
11A293loose thermal0.2410
22B375loose thermal1.2810
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 41 -
Rwork0.241 891 -
obs--99.04 %
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)
12.62350.17230.91931.5187-1.21587.181-0.0129-0.08280.0940.055-0.0826-0.0284-0.42650.59650.09550.06520.0034-0.00160.1088-0.01230.14442.121857.896536.587
25.59172.6711-4.97143.6142-3.48519.76570.1395-0.3714-0.10390.3061-0.3027-0.1822-0.03881.0610.16320.04840.0369-0.04230.2390.00390.164246.119249.253543.0263
32.2036-0.1631.651.76560.16735.9843-0.12820.04510.1212-0.1304-0.12040.0518-0.75920.10480.24850.12570.0208-0.01180.06670.00520.126832.259362.669323.7661
41.16860.13190.18927.06856.25518.54890.00060.10290.0472-0.4523-0.21090.1603-0.7853-0.56790.21030.09570.1009-0.02220.160.03490.186222.688559.242516.5364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 94
2X-RAY DIFFRACTION2B7 - 86
3X-RAY DIFFRACTION3C5 - 91
4X-RAY DIFFRACTION4D1 - 83

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