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- PDB-5azo: Crystal structure of a membrane protein from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5azo
TitleCrystal structure of a membrane protein from Pseudomonas aeruginosa
ComponentsMultidrug efflux outer membrane protein OprN
KeywordsMEMBRANE PROTEIN / Alpha barrel / Beta barrel
Function / homology
Function and homology information


efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / membrane
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Multidrug efflux outer membrane protein OprN
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYonehara, R. / Yamashita, E. / Nakagawa, A.
CitationJournal: Proteins / Year: 2016
Title: Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa.
Authors: Yonehara, R. / Yamashita, E. / Nakagawa, A.
History
DepositionOct 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug efflux outer membrane protein OprN


Theoretical massNumber of molelcules
Total (without water)49,6861
Polymers49,6861
Non-polymers00
Water0
1
A: Multidrug efflux outer membrane protein OprN

A: Multidrug efflux outer membrane protein OprN

A: Multidrug efflux outer membrane protein OprN


Theoretical massNumber of molelcules
Total (without water)149,0593
Polymers149,0593
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area16690 Å2
ΔGint-54 kcal/mol
Surface area56540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.501, 76.501, 191.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Multidrug efflux outer membrane protein OprN


Mass: 49686.188 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprN, PA2495 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0Y7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: MPD, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18601 / % possible obs: 100 % / Redundancy: 10.9 % / Net I/σ(I): 17.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WP1

1wp1


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.88 / SU B: 26.869 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.581 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27189 865 4.7 %RANDOM
Rwork0.23154 ---
obs0.23345 17736 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.58 Å2-0 Å2
2--1.16 Å20 Å2
3----3.75 Å2
Refinement stepCycle: 1 / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 0 0 3413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193460
X-RAY DIFFRACTIONr_bond_other_d0.0020.023325
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9664685
X-RAY DIFFRACTIONr_angle_other_deg0.92437586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.215443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93222.971175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.315578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2421548
X-RAY DIFFRACTIONr_chiral_restr0.0670.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
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_it1.4764.0521775
X-RAY DIFFRACTIONr_mcbond_other1.4724.051774
X-RAY DIFFRACTIONr_mcangle_it2.486.0742217
X-RAY DIFFRACTIONr_mcangle_other2.4816.0762218
X-RAY DIFFRACTIONr_scbond_it1.7724.3511685
X-RAY DIFFRACTIONr_scbond_other1.7724.3531686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0196.4312468
X-RAY DIFFRACTIONr_long_range_B_refined4.31231.8323794
X-RAY DIFFRACTIONr_long_range_B_other4.31231.8433795
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 64 -
Rwork0.307 1263 -
obs--99.4 %
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)
10.2520.07880.29040.21220.25321.4735-0.05860.00470.09780.00210.01370.1172-0.2095-0.14140.04490.04170.02760.00660.03390.01790.1178-16.073-29.0755-50.872
20.0084-0.0171-0.04170.1637-0.07410.71790.0081-0.01280.0116-0.01630.01430.022-0.18090.0083-0.02240.0535-0.0047-0.00240.0522-0.01810.0843-4.9988-33.4551-70.8217
30.02460.01670.01790.0964-0.06280.6070.0048-0.01710.0420.0269-0.00040.0114-0.1206-0.0408-0.00440.02780.00860.01040.0484-0.03680.0819-4.2753-31.1171-45.174
41.5199-1.2524-0.83481.16631.42134.56940.24690.2834-0.0613-0.0516-0.21140.04240.7469-0.1688-0.03550.2604-0.0107-0.03740.13970.03390.1065-15.3209-56.5237-84.9351
50.16650.0760.12190.132-0.12470.58980.0263-0.06510.01890.07910.00210.0594-0.089-0.1639-0.02840.0620.02410.04230.1052-0.01490.044-11.7665-37.3744-26.5732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION2A79 - 173
3X-RAY DIFFRACTION3A174 - 323
4X-RAY DIFFRACTION4A324 - 334
5X-RAY DIFFRACTION5A335 - 444

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