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- PDB-5aeo: Virulence-associated protein VapG from the intracellular pathogen... -

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Basic information

Entry
Database: PDB / ID: 5aeo
TitleVirulence-associated protein VapG from the intracellular pathogen Rhodococcus equi
ComponentsR. EQUI VAPG PROTEIN
KeywordsIMMUNE SYSTEM / BETA BARREL / BACTERIAL PATHOGEN / VIRULENCE PROTEIN / INTRACELLULAR PATHOGEN
Function / homology
Function and homology information


Rhodococcus equi virulence-associated protein / Rhodococcus equi virulence-associated protein / Rhodococcus equi virulence-associated superfamily / Rhodococcus equi virulence-associated protein / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Virulence associated protein VapG / R. equi VapG protein
Similarity search - Component
Biological speciesRHODOCOCCUS EQUI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOkoko, T. / Blagova, E.V. / Whittingham, J.L. / Dover, L.G. / Wilkinson, A.J.
CitationJournal: Vet.Microbiol. / Year: 2015
Title: Structural Characterisation of the Virulence-Associated Protein Vapg from the Horse Pathogen Rhodococcus Equi.
Authors: Okoko, T. / Blagova, E.V. / Whittingham, J.L. / Dover, L.G. / Wilkinson, A.J.
History
DepositionJan 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 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 / pdbx_struct_special_symmetry / 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_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R. EQUI VAPG PROTEIN
B: R. EQUI VAPG PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6553
Polymers34,6162
Non-polymers391
Water2,054114
1
A: R. EQUI VAPG PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3472
Polymers17,3081
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: R. EQUI VAPG PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,3081
Polymers17,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.550, 44.550, 259.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-157-

ALA

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Components

#1: Protein R. EQUI VAPG PROTEIN / VIRULENCE-ASSOCIATED PROTEIN G


Mass: 17307.805 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS EQUI (bacteria) / Strain: 103S / Plasmid: PET23B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EU62, UniProt: A0A3S5Y0Q5*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.72 Å3/Da / Density % sol: 29 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN SOLUTION: 30 MG/ML VAPG IN 10 MM TRIS-HCL PH 7.5, 10 MM NACL RESERVOIR: 0.3 M KCL, 20 % W/V PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Mar 17, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→31.5 Å / Num. obs: 24979 / % possible obs: 98 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / % possible all: 83

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CSB

4csb


Resolution: 1.8→31.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.943 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. C-TERMINAL PEPTIDE FRAGMENTS IN MOLECULES A AND B VIOLATE CRYSTALLOGRAPHIC SYMMETRY
RfactorNum. reflection% reflectionSelection details
Rfree0.23623 1267 5.1 %RANDOM
Rwork0.1991 ---
obs0.20094 23612 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.009 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 1 114 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191638
X-RAY DIFFRACTIONr_bond_other_d0.0070.021461
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.9252228
X-RAY DIFFRACTIONr_angle_other_deg0.89533355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43324.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64715215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
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_it3.1012.935875
X-RAY DIFFRACTIONr_mcbond_other3.0692.932874
X-RAY DIFFRACTIONr_mcangle_it3.9824.3781086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7183.329762
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 89 -
Rwork0.301 1420 -
obs--82.23 %

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