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- PDB-3zs6: The Structural characterization of Burkholderia pseudomallei OppA. -

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Basic information

Entry
Database: PDB / ID: 3zs6
TitleThe Structural characterization of Burkholderia pseudomallei OppA.
Components
  • OLIGOPEPTIDE DVA
  • PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
KeywordsPEPTIDE BINDING PROTEIN / ABC TRANSPORT SYSTEM
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
UNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLassaux, P. / Gourlay, L.J. / Bolognesi, M.
CitationJournal: Structure / Year: 2013
Title: A Structure-Based Strategy for Epitope Discovery in Burkholderia Pseudomallei Oppa Antigen.
Authors: Lassaux, P. / Peri, C. / Ferrer-Navarro, M. / Gourlay, L.J. / Gori, A. / Conchillo-Sole, O. / Rinchai, D. / Lertmemongkolchai, G. / Longhi, R. / Daura, X. / Colombo, G. / Bolognesi, M.
History
DepositionJun 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references / Structure summary
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
B: OLIGOPEPTIDE DVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4487
Polymers57,0442
Non-polymers4045
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12.4 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.860, 81.930, 74.180
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN


Mass: 56740.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96423 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q63ID0
#2: Protein/peptide OLIGOPEPTIDE DVA


Mass: 303.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) UNIDENTIFIED (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.79 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.5, 20% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→40.97 Å / Num. obs: 31801 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 20.29 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKA

1qka


Resolution: 2.1→38.464 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1604 5 %
Rwork0.1575 --
obs0.1602 31796 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.402 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.1885 Å20 Å23.095 Å2
2--1.9065 Å20 Å2
3----2.095 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 25 221 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064211
X-RAY DIFFRACTIONf_angle_d0.9095735
X-RAY DIFFRACTIONf_dihedral_angle_d12.7531570
X-RAY DIFFRACTIONf_chiral_restr0.063627
X-RAY DIFFRACTIONf_plane_restr0.004740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.25341390.15932734X-RAY DIFFRACTION100
2.1678-2.24530.23311550.15522736X-RAY DIFFRACTION100
2.2453-2.33520.21071500.14842726X-RAY DIFFRACTION100
2.3352-2.44140.2011310.15142733X-RAY DIFFRACTION100
2.4414-2.57010.24091340.15862761X-RAY DIFFRACTION100
2.5701-2.73110.23361360.16482725X-RAY DIFFRACTION100
2.7311-2.94190.2371380.162756X-RAY DIFFRACTION100
2.9419-3.23780.20551580.15812727X-RAY DIFFRACTION100
3.2378-3.7060.19711480.15782750X-RAY DIFFRACTION100
3.706-4.66790.1691520.14852760X-RAY DIFFRACTION100
4.6679-38.470.21631630.16832784X-RAY DIFFRACTION100
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)
11.5732-0.29350.02110.9459-0.26051.17790.0760.17850.0242-0.20730.01590.00410.0515-0.0979-0.05710.111-0.0122-0.0010.08610.01480.066813.9567-9.97174.7849
21.0899-0.3881-0.21390.5373-0.01280.9103-0.0297-0.15410.14160.09370.1146-0.0724-0.1573-0.0369-0.04120.08930.0449-0.01250.0867-0.02950.093412.4727-2.161329.6793
35.8118-3.23966.2475.3056-2.07477.5178-0.4528-0.1102-0.3267-0.3464-0.4628-1.17290.44521.36490.95670.11610.00480.03150.18730.03370.207212.2394-7.546420.2648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 48:274)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 275:553)
3X-RAY DIFFRACTION3CHAIN B

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