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- PDB-2f1t: Outer membrane protein OmpW -

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Basic information

Entry
Database: PDB / ID: 2f1t
TitleOuter membrane protein OmpW
ComponentsOuter membrane protein W
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta barrel
Function / homology
Function and homology information


cell outer membrane / transmembrane transport
Similarity search - Function
Outer membrane protein, OmpW / OmpW family / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein W
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å
Authorsvan den Berg, B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The outer membrane protein OmpW forms an eight-stranded beta-barrel with a hydrophobic channel.
Authors: Hong, H. / Patel, D.R. / Tamm, L.K. / van den Berg, B.
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 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: Outer membrane protein W
B: Outer membrane protein W
C: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,51617
Polymers65,1003
Non-polymers3,41614
Water00
1
A: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5548
Polymers21,7001
Non-polymers1,8547
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6345
Polymers21,7001
Non-polymers9344
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3284
Polymers21,7001
Non-polymers6283
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.158, 82.158, 186.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Outer membrane protein W


Mass: 21700.102 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ompW / Plasmid: pB22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: P0A915
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 9
Details: 28-32% PEG400, 0.2 M CaCl2, 50 mM glycine, pH 9, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A11.1
SYNCHROTRONNSLS X6A21.38
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 2005 / Details: Si(111) channel cut monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) channel cut monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) channel cut monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.381
ReflectionResolution: 2.45→46.8 Å / Num. all: 14337 / Num. obs: 14157 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 38.4
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2678 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS
Starting model: none

Resolution: 3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 733 -random
Rwork0.274 ---
all0.276 14337 --
obs0.276 14157 98.7 %-
Displacement parametersBiso mean: 71.39 Å2
Baniso -1Baniso -2Baniso -3
1-24.48 Å213.26 Å20 Å2
2--24.48 Å20 Å2
3----48.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 234 0 4518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_improper_angle_d0.94
LS refinement shellResolution: 3→3.13 Å / Rfactor Rfree error: 0.043
RfactorNum. reflection% reflection
Rfree0.414 94 -
Rwork0.363 --
obs-1754 98.8 %

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