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- PDB-4rjx: Crystal structure of the OprO mutant protein F62Y/D114Y -

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Basic information

Entry
Database: PDB / ID: 4rjx
TitleCrystal structure of the OprO mutant protein F62Y/D114Y
ComponentsPorin O
KeywordsMEMBRANE PROTEIN / beta barrel / outer membrane protein / polyphosphate uptake channel
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Phosphate-selective porin O/P / Phosphate-selective porin O and P / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Porin O
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
Authorsvan den Berg, B.
CitationJournal: Biophys.J. / Year: 2015
Title: Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa.
Authors: Modi, N. / Ganguly, S. / Barcena-Uribarri, I. / Benz, R. / van den Berg, B. / Kleinekathofer, U.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Porin O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6746
Polymers47,3541
Non-polymers1,3215
Water8,431468
1
A: Porin O
hetero molecules

A: Porin O
hetero molecules

A: Porin O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,02318
Polymers142,0613
Non-polymers3,96215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16100 Å2
ΔGint-67 kcal/mol
Surface area48850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.479, 87.479, 159.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

21A-975-

HOH

31A-976-

HOH

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Components

#1: Protein Porin O


Mass: 47353.715 Da / Num. of mol.: 1 / Fragment: UNP residues 25-438 / Mutation: F62Y, D114Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprO, PA3280 / Production host: Escherichia coli (E. coli) / References: UniProt: P32977
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 50 mM sodium acetate, 0.225 M ammonium sulphate, 12% PEG4000, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 10, 2013
RadiationMonochromator: single bounce Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.54→29.3 Å / Num. all: 67316 / Num. obs: 67047 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.54→1.58 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→29.3 Å / SU ML: 0.16 / σ(F): 1.96 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 3393 5.06 %copied from wild type OprO dataset (4RJW)
Rwork0.1542 ---
obs0.1555 67025 99.58 %-
all-67316 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 34 468 3819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063483
X-RAY DIFFRACTIONf_angle_d1.084727
X-RAY DIFFRACTIONf_dihedral_angle_d12.9131248
X-RAY DIFFRACTIONf_chiral_restr0.049490
X-RAY DIFFRACTIONf_plane_restr0.005626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.56090.30361410.26062575X-RAY DIFFRACTION96
1.5609-1.58420.23761240.24352589X-RAY DIFFRACTION98
1.5842-1.6090.29851400.23022641X-RAY DIFFRACTION99
1.609-1.63530.27241510.22122625X-RAY DIFFRACTION100
1.6353-1.66350.2261540.21272655X-RAY DIFFRACTION100
1.6635-1.69380.2361420.19742647X-RAY DIFFRACTION100
1.6938-1.72640.2271030.18772702X-RAY DIFFRACTION100
1.7264-1.76160.20921350.17852627X-RAY DIFFRACTION100
1.7616-1.79990.23551410.17082686X-RAY DIFFRACTION100
1.7999-1.84180.1931600.1612639X-RAY DIFFRACTION100
1.8418-1.88780.19771490.15482647X-RAY DIFFRACTION100
1.8878-1.93880.16731470.15472697X-RAY DIFFRACTION100
1.9388-1.99590.16991380.13672638X-RAY DIFFRACTION100
1.9959-2.06030.18481300.13382661X-RAY DIFFRACTION100
2.0603-2.13390.16361390.13492678X-RAY DIFFRACTION100
2.1339-2.21930.15281490.13372674X-RAY DIFFRACTION100
2.2193-2.32030.17551530.13452627X-RAY DIFFRACTION100
2.3203-2.44250.17911320.1492699X-RAY DIFFRACTION100
2.4425-2.59550.18371230.14542650X-RAY DIFFRACTION100
2.5955-2.79570.17691330.14782672X-RAY DIFFRACTION100
2.7957-3.07680.161590.14622646X-RAY DIFFRACTION100
3.0768-3.52140.15261480.1422649X-RAY DIFFRACTION100
3.5214-4.43410.17241430.13662657X-RAY DIFFRACTION100
4.4341-29.33320.15431590.16332651X-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)
10.273-0.0514-0.05150.0667-0.07920.1820.02710.1017-0.062-0.04140.0078-0.02960.0723-0.01960.00040.16370.0042-0.02340.169-0.00440.12451.92121.93260.8399
20.23460.0585-0.02240.21310.05050.1935-0.00840.03420.0404-0.00760.01030.0244-0.0546-0.015400.12180.0046-0.00920.10250.00920.1152-7.368818.797420.2286
30.07760.06930.06790.05430.0670.08270.0314-0.02080.11720.0033-0.00740.0362-0.0575-0.0665-0.00910.19310.02550.00320.1360.01080.1715-10.897828.022129.9278
40.27910.0630.1480.1970.0590.1379-0.00910.01170.07170.0003-0.00130.0151-0.122-0.005200.16580.00270.00120.09410.010.13230.5330.962522.3958
50.0698-0.041-0.05230.02220.02220.0134-0.0503-0.02040.0139-0.01670.010.0195-0.12510.0916-00.1657-0.0104-0.01330.1373-0.00030.13811.713324.929523.8422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -10:46 )A-10 - 46
2X-RAY DIFFRACTION2( CHAIN A AND RESID 47:245 )A47 - 245
3X-RAY DIFFRACTION3( CHAIN A AND RESID 246:271 )A246 - 271
4X-RAY DIFFRACTION4( CHAIN A AND RESID 272:375 )A272 - 375
5X-RAY DIFFRACTION5( CHAIN A AND RESID 376:414 )A376 - 414

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