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- PDB-5dlb: Crystal structure of chaperone EspG3 of ESX-3 type VII secretion ... -

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Basic information

Entry
Database: PDB / ID: 5dlb
TitleCrystal structure of chaperone EspG3 of ESX-3 type VII secretion system from Mycobacterium marinum M
Componentschaperone EspG3
KeywordsCHAPERONE / virulence / ESX / secretion / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homologyEspG family / EspG family / : / THIOCYANATE ION / Conserved protein
Function and homology information
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsChan, S. / Arbing, M.A. / Kim, J. / Kahng, S. / Sawaya, M.R. / Eisenberg, D.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems.
Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / ...Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / Parret, A.H.A. / Korotkov, K.V.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Structure summary
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chaperone EspG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,93545
Polymers34,1171
Non-polymers3,81844
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.206, 46.019, 58.006
Angle α, β, γ (deg.)90.000, 92.240, 90.000
Int Tables number5
Space group name H-MC121
DetailsMonomer according to Gel filtration

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Components

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Protein , 1 types, 1 molecules A

#1: Protein chaperone EspG3


Mass: 34117.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_0548 / Plasmid: pMAPLe4 / Details (production host): pET28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: B2HNX0

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Non-polymers , 6 types, 109 molecules

#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Pt
#6: Chemical...
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1uL 21.5mg/mL protein plus 0.5uL reservoir solution drop against 500uL reservoir solution of 1.45M ammonium sulfate, 200mM lithium sulfate, 70mM CAPS pH10.5, microseeded

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0702 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0702 Å / Relative weight: 1
ReflectionResolution: 1.77→57.96 Å / Num. all: 25746 / Num. obs: 25746 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 37.98 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.063 / Χ2: 1.091 / Net I/σ(I): 12.6 / Num. measured all: 137146
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
1.77-1.873.40.0980.8271.4125611631287713.92490
1.55-1.660.1821.6460.392298515254129792.22185.1
1.66-1.790.480.7040.982090914225119300.95383.9
1.79-1.960.8810.2782.532000513075113150.37886.5
1.96-2.190.9740.1115.871768611857101190.15185.3
2.19-2.530.9870.06610.1157431040190130.09186.7
2.53-3.10.9940.04115.2712735881673840.05783.8
3.1-4.370.9960.03219.969301679554390.04480
4.37-57.960.9950.0322.085221375830430.04381

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→57.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2606 / WRfactor Rwork: 0.2238 / FOM work R set: 0.6999 / SU B: 9.631 / SU ML: 0.138 / SU R Cruickshank DPI: 0.1444 / SU Rfree: 0.1361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1310 5.1 %RANDOM
Rwork0.2089 ---
obs0.2108 24426 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.04 Å2 / Biso mean: 37.986 Å2 / Biso min: 22.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0 Å2-1.24 Å2
2---2.21 Å2-0 Å2
3---3.31 Å2
Refinement stepCycle: final / Resolution: 1.77→57.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 140 65 2150
Biso mean--72.71 47.11 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022085
X-RAY DIFFRACTIONr_bond_other_d0.0020.021922
X-RAY DIFFRACTIONr_angle_refined_deg2.131.9822791
X-RAY DIFFRACTIONr_angle_other_deg0.97634386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5322.63276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81415278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4741516
X-RAY DIFFRACTIONr_chiral_restr0.1140.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_mcbond_it1.6711.011081
X-RAY DIFFRACTIONr_mcbond_other0.9880.8191048
X-RAY DIFFRACTIONr_mcangle_it1.6641.2221306
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 82 -
Rwork0.427 1826 -
all-1908 -
obs--89.03 %
Refinement TLS params.Method: refined / Origin x: 22.6063 Å / Origin y: 43.8457 Å / Origin z: -14.0014 Å
111213212223313233
T0.3005 Å2-0.0239 Å20.052 Å2-0.4507 Å2-0.0174 Å2--0.0143 Å2
L2.6679 °2-1.402 °21.3327 °2-1.6963 °2-0.8516 °2--1.3528 °2
S0.0004 Å °0.2165 Å °0.0706 Å °-0.1233 Å °-0.0731 Å °-0.0478 Å °-0.0163 Å °0.0664 Å °0.0726 Å °

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