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- PDB-4usx: The Structure of the C-terminal YadA-like domain of BPSL2063 from... -

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Basic information

Entry
Database: PDB / ID: 4usx
TitleThe Structure of the C-terminal YadA-like domain of BPSL2063 from Burkholderia pseudomallei
ComponentsTRIMERIC AUTOTRANSPORTER ADHESIN
KeywordsTRANSPORT PROTEIN / YADA-LIKE HEAD DOMAIN
Function / homology
Function and homology information


cell outer membrane / protein transport / cell surface / metal ion binding
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Serralysin-like metalloprotease, C-terminal / Pilin-like / Mainly Beta
Similarity search - Domain/homology
Biological speciesBURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPerletti, L. / Gourlay, L.J. / Peano, C. / Pietrelli, A. / DeBellis, G. / Deantonio, C. / Santoro, C. / Sblattero, D. / Bolognesi, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Selecting Soluble/Foldable Protein Domains Through Single-Gene or Genomic Orf Filtering: Structure of the Head Domain of Burkholderia Pseudomallei Antigen Bpsl2063.
Authors: Gourlay, L.J. / Peano, C. / Deantonio, C. / Perletti, L. / Pietrelli, A. / Villa, R. / Matterazzo, E. / Lassaux, P. / Santoro, C. / Puccio, S. / Sblattero, D. / Bolognesi, M.
History
DepositionJul 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIMERIC AUTOTRANSPORTER ADHESIN
B: TRIMERIC AUTOTRANSPORTER ADHESIN
C: TRIMERIC AUTOTRANSPORTER ADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,68710
Polymers107,5173
Non-polymers1707
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25480 Å2
ΔGint-233 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.115, 58.852, 74.407
Angle α, β, γ (deg.)90.00, 104.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.4774, 0.4752, 0.7391), (-0.5648, -0.4784, 0.6724), (0.6731, -0.7385, 0.04)1.9125, -1.116, 31.0281
2given(0.4665, -0.5555, 0.6884), (0.4647, -0.5083, -0.7251), (0.7526, 0.6581, 0.021)1.6088, 1.4848, 31.6326

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Components

#1: Protein TRIMERIC AUTOTRANSPORTER ADHESIN


Mass: 35838.844 Da / Num. of mol.: 3
Fragment: YADA-LIKE COLLAGEN BINDING DOMAIN, UNP RESIDUES 657-992
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
Plasmid: PET21B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q63TA4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.18 Å3/Da / Density % sol: 43.74 % / Description: NONE
Crystal growpH: 4
Details: PACT PREMIER (MOLECULAR DIMENSIONS) CONDITION D1 (0.1M MALIC ACID, MES AND TRIS (MMT) BUFFER PH 4.0, 25% PEG1500. CRYSTALS WERE CRYOCOOLED IN MOTHER LIQUOR CONTAINING 40% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 48598 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LAA

3laa


Resolution: 1.8→39.69 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 21.47 / Stereochemistry target values: ML
Details: PROTEOLYSIS OCCURRED DURING RESULTING IN THE LOSS OF APPROX 136 C-TERMINAL RESIDUES
RfactorNum. reflection% reflection
Rfree0.2042 2460 5.1 %
Rwork0.1685 --
obs0.1703 48564 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 7 448 4740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074344
X-RAY DIFFRACTIONf_angle_d1.0225955
X-RAY DIFFRACTIONf_dihedral_angle_d11.8171446
X-RAY DIFFRACTIONf_chiral_restr0.044737
X-RAY DIFFRACTIONf_plane_restr0.005803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.83470.29091080.24942267X-RAY DIFFRACTION88
1.8347-1.87210.26561360.23332427X-RAY DIFFRACTION94
1.8721-1.91280.2881390.21672545X-RAY DIFFRACTION99
1.9128-1.95730.24241350.19552599X-RAY DIFFRACTION100
1.9573-2.00630.23991240.18372531X-RAY DIFFRACTION100
2.0063-2.06050.23161220.17942626X-RAY DIFFRACTION100
2.0605-2.12110.18771300.16292553X-RAY DIFFRACTION100
2.1211-2.18960.19331400.16522605X-RAY DIFFRACTION100
2.1896-2.26790.2111250.15352582X-RAY DIFFRACTION100
2.2679-2.35860.18411440.152570X-RAY DIFFRACTION100
2.3586-2.4660.18891480.15912574X-RAY DIFFRACTION100
2.466-2.5960.24491440.1722558X-RAY DIFFRACTION100
2.596-2.75860.19711540.16822585X-RAY DIFFRACTION100
2.7586-2.97150.20911220.1762637X-RAY DIFFRACTION100
2.9715-3.27040.22121280.17462585X-RAY DIFFRACTION100
3.2704-3.74330.21011650.16272589X-RAY DIFFRACTION100
3.7433-4.7150.15981490.142608X-RAY DIFFRACTION100
4.715-39.69930.16971470.15912663X-RAY DIFFRACTION100

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