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- PDB-4rlc: Crystal structure of the N-terminal beta-barrel domain of Pseudom... -

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Basic information

Entry
Database: PDB / ID: 4rlc
TitleCrystal structure of the N-terminal beta-barrel domain of Pseudomonas aeruginosa OprF
ComponentsOuter membrane porin F
KeywordsTRANSPORT PROTEIN / outer membrane protein / beta-barrel
Function / homology
Function and homology information


adhesion of symbiont to host / complement component C3b binding / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / regulation of cell shape / calcium ion binding
Similarity search - Function
Outer membrane porin F, N-terminal / OprF membrane domain / TSP type-3 repeat / Porin - #20 / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...Outer membrane porin F, N-terminal / OprF membrane domain / TSP type-3 repeat / Porin - #20 / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZahn, M. / Basle, A. / van den Berg, B.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Small-Molecule Transport by CarO, an Abundant Eight-Stranded beta-Barrel Outer Membrane Protein from Acinetobacter baumannii.
Authors: Zahn, M. / D'Agostino, T. / Eren, E. / Basle, A. / Ceccarelli, M. / van den Berg, B.
History
DepositionOct 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Feb 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

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Assembly

Deposited unit
A: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6998
Polymers19,5541
Non-polymers2,1457
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.009, 26.779, 54.892
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Outer membrane porin F


Mass: 19553.502 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 25-184)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: oprF, PA1777 / Production host: Escherichia coli (E. coli) / References: UniProt: P13794
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 33% PEG200, 0.2 M ammonium sulfate, 0.02 M sodium chloride, 0.02 M sodium citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.6→54.612 Å / Num. obs: 20209 / % possible obs: 99.6 %
Reflection shellResolution: 1.6→1.63 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
REFMAC5.8.0073refinement
XDSdata reduction
XDS/ XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→54.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.231 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22879 1022 5.1 %RANDOM
Rwork0.18853 ---
obs0.19065 19182 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.718 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å20 Å2-0.42 Å2
2--4.6 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→54.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 87 29 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191157
X-RAY DIFFRACTIONr_bond_other_d0.0010.021107
X-RAY DIFFRACTIONr_angle_refined_deg2.041.9841526
X-RAY DIFFRACTIONr_angle_other_deg0.80232544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2475133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63724.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35815160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.827153
X-RAY DIFFRACTIONr_chiral_restr0.130.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
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_it1.9291.611541
X-RAY DIFFRACTIONr_mcbond_other1.9271.611540
X-RAY DIFFRACTIONr_mcangle_it2.8392.374671
X-RAY DIFFRACTIONr_mcangle_other2.8382.375672
X-RAY DIFFRACTIONr_scbond_it4.0212.662616
X-RAY DIFFRACTIONr_scbond_other4.0182.664617
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1843.61856
X-RAY DIFFRACTIONr_long_range_B_refined8.13515.4681114
X-RAY DIFFRACTIONr_long_range_B_other8.13315.491115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 81 -
Rwork0.301 1371 -
obs--99.11 %
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)
11.4408-0.0565-0.61680.3329-0.15050.9470.0138-0.0228-0.0815-0.0368-0.02740.0461-0.0095-0.13870.01350.09540.01010.0010.0484-0.01170.141510.80782.383527.1627
27.0276-1.2071-2.01020.20740.35758.14630.06040.5701-0.1616-0.0092-0.09810.02810.0866-0.18490.03770.0185-0.00390.0070.0576-0.02380.015211.67642.589310.0426
31.83340.1167-0.21670.258-0.24580.2422-0.02450.1115-0.1917-0.01520.04530.02990.0272-0.0499-0.02080.0775-0.0078-0.00630.0146-0.01460.09987.408-1.883326.6947
42.721-0.8022-4.42051.3021.19377.21740.0799-0.10910.1041-0.01290.0821-0.1533-0.10180.1405-0.16210.0424-0.015-0.00530.1606-0.00530.01955.10352.6862-1.8498
52.4155-0.101-0.05370.3693-0.12440.04630.0032-0.0025-0.2218-0.0007-0.0272-0.0736-0.00790.00780.0240.09590.00380.01320.0104-0.00660.131611.0905-3.402824.5189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 45
2X-RAY DIFFRACTION2A46 - 68
3X-RAY DIFFRACTION3A69 - 99
4X-RAY DIFFRACTION4A100 - 109
5X-RAY DIFFRACTION5A110 - 160

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