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- PDB-7jqe: Structure of an extracellular fragment of EsaA from Streptococcus... -

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Basic information

Entry
Database: PDB / ID: 7jqe
TitleStructure of an extracellular fragment of EsaA from Streptococcus gallolyticus
ComponentsESAT-6/WXG100 secretion system protein
KeywordsPROTEIN TRANSPORT / Bacterial type VII secretion system / bacterial toxin transport / membrane protein
Function / homologyType VII secretion system EsaA / membrane => GO:0016020 / plasma membrane / ESAT-6/WXG100 secretion system protein
Function and homology information
Biological speciesStreptococcus gallolyticus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKlein, T.A. / Grebenc, D.W. / Kim, Y. / Whitney, J.C.
CitationJournal: Structure / Year: 2021
Title: Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA.
Authors: Klein, T.A. / Grebenc, D.W. / Gandhi, S.Y. / Shah, V.S. / Kim, Y. / Whitney, J.C.
History
DepositionAug 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESAT-6/WXG100 secretion system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,53125
Polymers66,0681
Non-polymers1,46324
Water50428
1
A: ESAT-6/WXG100 secretion system protein
hetero molecules

A: ESAT-6/WXG100 secretion system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,06150
Polymers132,1352
Non-polymers2,92648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area16450 Å2
ΔGint11 kcal/mol
Surface area34310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.466, 248.235, 81.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-827-

HOH

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Components

#1: Protein ESAT-6/WXG100 secretion system protein


Mass: 66067.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gallolyticus (strain ATCC 43143 / F-1867) (bacteria)
Strain: ATCC 43143 / F-1867 / Gene: esaA, SGGB_0524 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus / References: UniProt: F5WZF6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 0.1M Tris-HCl pH 7.0, 10% (w/v) PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→55.3 Å / Num. obs: 29568 / % possible obs: 98.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 51.38 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.069 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1 / Num. unique obs: 1310 / CC1/2: 0.513 / Rpim(I) all: 0.644 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
HKL-3000phasing
PHENIXphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→41.37 Å / SU ML: 0.3407 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.7526
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2616 1475 5.05 %
Rwork0.2146 27731 -
obs0.2169 29206 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 93 28 2837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252816
X-RAY DIFFRACTIONf_angle_d0.42743782
X-RAY DIFFRACTIONf_chiral_restr0.0363462
X-RAY DIFFRACTIONf_plane_restr0.0022481
X-RAY DIFFRACTIONf_dihedral_angle_d15.78681020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.43371260.37492224X-RAY DIFFRACTION88.78
2.48-2.570.35351210.33292429X-RAY DIFFRACTION95.04
2.57-2.670.29941360.29512471X-RAY DIFFRACTION97.93
2.67-2.790.32221200.2712554X-RAY DIFFRACTION98.89
2.79-2.940.34881430.25782517X-RAY DIFFRACTION98.88
2.94-3.120.29881350.25172540X-RAY DIFFRACTION99.29
3.12-3.360.26661530.23132533X-RAY DIFFRACTION99.44
3.36-3.70.23851410.2062574X-RAY DIFFRACTION99.41
3.7-4.230.21331320.18562591X-RAY DIFFRACTION99.52
4.24-5.330.23991190.1712604X-RAY DIFFRACTION99.23
5.34-41.370.24371490.19552694X-RAY DIFFRACTION98.27
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)
11.071611684230.0502372068916-0.05222338133863.670107605280.2225238143560.593554228465-0.0958686069617-0.0340118294119-0.4758976043460.298709861269-0.002164124044580.3585836843750.19367066473-0.03796283019740.01490536115940.726428033893-0.02065480556190.072422315530.3727776654010.04429432472610.4543617001467.9913979929-35.475629553764.2222538642
20.8467929404870.0184267011852-0.09828335938353.848690730410.07672035601580.260031460167-0.07625825979870.0001531776530960.201886327745-0.1759433261320.05944360971770.433598985005-0.0643108966828-0.0447334670420.006251388090770.7213840144850.00562907857193-0.07308264110370.362648527764-0.003597576690450.34704216444568.402081729611.172285470162.0325605162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 96 through 267 )
2X-RAY DIFFRACTION2chain 'A' and (resid 268 through 494 )

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