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- PDB-6rgn: BteA131 -

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Basic information

Entry
Database: PDB / ID: 6rgn
TitleBteA131
ComponentsDUF3120 domain-containing protein
KeywordsLIPID BINDING PROTEIN / PIP2 effector Type three secretion system Bordetella
Function / homologyProtein of unknown function DUF3220 / DUF3220 superfamily / Protein of unknown function (DUF3120) / DUF3120 domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsDavidov, G. / Zarivach, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
European CommissionPIRG4-GA-2008-239182 T3SSBteA Israel
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2019
Title: Structure and membrane-targeting of a Bordetella pertussis effector N-terminal domain.
Authors: Yahalom, A. / Davidov, G. / Kolusheva, S. / Shaked, H. / Barber-Zucker, S. / Zarivach, R. / Chill, J.H.
History
DepositionApr 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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.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.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: DUF3120 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2786
Polymers16,8711
Non-polymers4075
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-62 kcal/mol
Surface area5650 Å2
Unit cell
Length a, b, c (Å)51.428, 51.428, 82.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-205-

NA

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Components

#1: Protein DUF3120 domain-containing protein / Protein of uncharacterized function (DUF3120)


Mass: 16870.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: EHO76_17700, NCTC10911_04001
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A381ABV9, UniProt: Q7VSD3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate pH 4.5 and 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.01→43.67 Å / Num. obs: 7548 / % possible obs: 100 % / Redundancy: 25.8 % / Net I/σ(I): 79.26
Reflection shellResolution: 2.01→2.059 Å / Num. unique obs: 390

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→36.39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.616 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23226 433 5.6 %RANDOM
Rwork0.17259 ---
obs0.17604 7283 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2--0.12 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.01→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 21 92 872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013806
X-RAY DIFFRACTIONr_bond_other_d0.0010.017716
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.6421090
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5821660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.552596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42320.67859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45815143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5411511
X-RAY DIFFRACTIONr_chiral_restr0.1010.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02907
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02182
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_it0.8731.056375
X-RAY DIFFRACTIONr_mcbond_other0.8681.052374
X-RAY DIFFRACTIONr_mcangle_it1.4681.57468
X-RAY DIFFRACTIONr_mcangle_other1.4671.575469
X-RAY DIFFRACTIONr_scbond_it1.6671.344430
X-RAY DIFFRACTIONr_scbond_other1.3121.26412
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1051.85596
X-RAY DIFFRACTIONr_long_range_B_refined5.40514.316951
X-RAY DIFFRACTIONr_long_range_B_other5.21313.549928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.007→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 34 -
Rwork0.101 542 -
obs--99.65 %
Refinement TLS params.Method: refined / Origin x: 11.481 Å / Origin y: 6.6866 Å / Origin z: -9.6967 Å
111213212223313233
T0.0701 Å20.0295 Å20.0023 Å2-0.0629 Å2-0.0071 Å2--0.0046 Å2
L3.468 °21.8121 °20.9104 °2-3.9173 °20.8988 °2--2.2709 °2
S-0.097 Å °0.2505 Å °-0.0486 Å °-0.2385 Å °0.0699 Å °0.0453 Å °0.0117 Å °-0.0891 Å °0.027 Å °

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