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- PDB-8jto: Outer membrane porin of Burkholderia pseudomallei (BpsOmp38) in c... -

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Basic information

Entry
Database: PDB / ID: 8jto
TitleOuter membrane porin of Burkholderia pseudomallei (BpsOmp38) in complex with ceftazidime
ComponentsOuter membrane porin (Fragment)
KeywordsPROTEIN TRANSPORT / Burkholderia pseudomallei / Outer membrane protein / Porin / Transport protein
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, Neisseria sp. type / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
ACYLATED CEFTAZIDIME / Outer membrane porin
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBunkum, P. / Aunkham, A. / Bert van den, B. / Robinson, R.C. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To be published
Title: Structure and function of outer membrane protein from Burkholderia pseudomallei (BpsOmp38)
Authors: Bunkum, P. / Aunkham, A. / Bert van den, B. / Robinson, R.C. / Suginta, W.
History
DepositionJun 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 23, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / cell / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / space_group / space_group_symop / struct_asym / struct_conn / struct_sheet_range / symmetry
Item: _atom_type.scat_Cromer_Mann_a1 / _atom_type.scat_Cromer_Mann_a2 ..._atom_type.scat_Cromer_Mann_a1 / _atom_type.scat_Cromer_Mann_a2 / _atom_type.scat_Cromer_Mann_b1 / _atom_type.scat_Cromer_Mann_b2 / _atom_type.scat_Cromer_Mann_c / _atom_type.scat_source / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entry_details.has_protein_modification / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Ligand identity
Details: The model was re-refined, and the ceftazidime ligand was added and refined based on the electron-density map.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane porin (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,31514
Polymers38,0181
Non-polymers3,29613
Water3,585199
1
A: Outer membrane porin (Fragment)
hetero molecules

A: Outer membrane porin (Fragment)
hetero molecules

A: Outer membrane porin (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,94442
Polymers114,0543
Non-polymers9,88939
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area18900 Å2
ΔGint-183 kcal/mol
Surface area40440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.045, 151.045, 49.099
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-411-

NA

21A-412-

NA

31A-610-

HOH

41A-656-

HOH

51A-685-

HOH

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Components

#1: Protein Outer membrane porin (Fragment)


Mass: 38018.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: omp38 / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli C43 (DE3) / References: UniProt: Q7WZL2
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.25 Å3/Da / Density % sol: 71.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.5 M Sodium Chloride, 0.05 M Calcium Chloride dihydrate, 0.1 M MES, pH6.5, and 37% w/v PEG 400

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2020 / Details: LN2-Cooled, Fixed-Exit
RadiationMonochromator: LN2-Cooled, Fixed-Exit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.249→19.95 Å / Num. obs: 27951 / % possible obs: 87.4 % / Redundancy: 2.3 % / CC1/2: 0.993 / CC star: 0.998 / Net I/σ(I): 11.1
Reflection shellResolution: 2.25→2.25 Å / Num. unique obs: 30807 / CC1/2: 0.832

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→19.95 Å / SU ML: 0.2118 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2164 1359 4.87 %
Rwork0.1736 26567 -
obs0.1756 27926 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.11 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 115 199 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332754
X-RAY DIFFRACTIONf_angle_d0.67973710
X-RAY DIFFRACTIONf_chiral_restr0.048382
X-RAY DIFFRACTIONf_plane_restr0.0054487
X-RAY DIFFRACTIONf_dihedral_angle_d17.3496983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.330.24571170.18422120X-RAY DIFFRACTION73.54
2.33-2.420.20821310.17992508X-RAY DIFFRACTION86.81
2.42-2.530.23951410.1812621X-RAY DIFFRACTION90.86
2.53-2.670.21521250.17552612X-RAY DIFFRACTION89.36
2.67-2.830.24971510.16792755X-RAY DIFFRACTION95.47
2.83-3.050.19671420.16872814X-RAY DIFFRACTION95.82
3.05-3.360.20391390.16252795X-RAY DIFFRACTION95.82
3.36-3.840.20691400.16362782X-RAY DIFFRACTION94.84
3.84-4.820.20111590.17452743X-RAY DIFFRACTION93.52
4.83-19.950.24171140.18642817X-RAY DIFFRACTION91.91

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