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- PDB-4xwp: Structure of PE-PPE domains of ESX-1 secreted protein EspB, C2221... -

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Basic information

Entry
Database: PDB / ID: 4xwp
TitleStructure of PE-PPE domains of ESX-1 secreted protein EspB, C2221 in presence of Ca
ComponentsESX-1 secretion-associated protein EspB
KeywordsPROTEIN TRANSPORT / ESX-1 / type VII secretion system / secreted protein / PE domain / PPE domain
Function / homologyESX-1 secretion-associated protein EspB, PE domain / ESX-1 secreted protein B PE domain / protein secretion by the type VII secretion system / PPE superfamily / biological process involved in interaction with host / extracellular region / identical protein binding / ESX-1 secretion-associated protein EspB
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsKorotkov, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structure of EspB, a secreted substrate of the ESX-1 secretion system of Mycobacterium tuberculosis.
Authors: Korotkova, N. / Piton, J. / Wagner, J.M. / Boy-Rottger, S. / Japaridze, A. / Evans, T.J. / Cole, S.T. / Pojer, F. / Korotkov, K.V.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-1 secretion-associated protein EspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0292
Polymers29,9891
Non-polymers401
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.240, 69.510, 119.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-648-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein ESX-1 secretion-associated protein EspB / Antigen MTB48


Mass: 29989.094 Da / Num. of mol.: 1 / Fragment: UNP residues 7-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: espB, mtb48, Rv3881c, MTV027.16c / Plasmid: pRSF-NT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P9WJD9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M calcium acetate, 0.1M Tris-HCl, 20% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→59.57 Å / Num. all: 25053 / Num. obs: 25045 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 37.171 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Χ2: 1.023 / Net I/σ(I): 17.81 / Num. measured all: 172885
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.82-1.920.8450.9452.3912809183318331.14100
1.87-1.920.880.8352.6212640180618060.903100
1.92-1.970.9160.633.4711980170817070.6899.9
1.97-2.030.9520.4594.5811724167616760.496100
2.03-2.10.9640.375.6311577165416540.4100
2.1-2.180.9830.2617.6511138158515850.282100
2.18-2.260.9880.1999.6610538150215020.215100
2.26-2.350.9910.15412.0410321147414740.166100
2.35-2.450.9960.11514.869990142214220.124100
2.45-2.570.9960.09916.979496136613660.107100
2.57-2.710.9970.07821.18839127112710.084100
2.71-2.880.9980.06124.998598124112410.066100
2.88-3.080.9980.05327.927862114211420.057100
3.08-3.320.9990.04333.117468109410940.047100
3.32-3.640.9990.03739.8867039999990.04100
3.64-4.070.9990.03145.4760819109100.034100
4.07-4.70.9990.02948.8153268048040.032100
4.7-5.760.9990.02750.1445146926910.02999.9
5.76-8.140.9990.02751.9134795505500.03100
8.140.9990.02950.8518023243180.03298.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G38

2g38


Resolution: 1.82→59.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2333 / WRfactor Rwork: 0.2011 / FOM work R set: 0.8031 / SU B: 3.592 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1322 / SU Rfree: 0.1263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1264 5 %RANDOM
Rwork0.1988 23783 --
obs0.2006 23783 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.3 Å2 / Biso mean: 37.72 Å2 / Biso min: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å20 Å2
2---3.73 Å20 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 1.82→59.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 1 159 2010
Biso mean--56.76 43.45 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191900
X-RAY DIFFRACTIONr_bond_other_d0.0010.021788
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9542587
X-RAY DIFFRACTIONr_angle_other_deg0.89434106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9135239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60624.94999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85315315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5021515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_mcbond_it1.9043.525947
X-RAY DIFFRACTIONr_mcbond_other1.9023.524946
X-RAY DIFFRACTIONr_mcangle_it2.6495.2661180
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 90 -
Rwork0.33 1738 -
all-1828 -
obs--100 %

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