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- PDB-2f1v: Outer membrane protein OmpW -

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Basic information

Entry
Database: PDB / ID: 2f1v
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
D: Outer membrane protein W
E: Outer membrane protein W
F: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,75312
Polymers130,2016
Non-polymers5536
Water00
1
A: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7922
Polymers21,7001
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7922
Polymers21,7001
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7922
Polymers21,7001
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7922
Polymers21,7001
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7922
Polymers21,7001
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7922
Polymers21,7001
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
A: Outer membrane protein W
B: Outer membrane protein W
F: Outer membrane protein W
hetero molecules

C: Outer membrane protein W
D: Outer membrane protein W
E: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,75312
Polymers130,2016
Non-polymers5536
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area10830 Å2
ΔGint-79 kcal/mol
Surface area45690 Å2
MethodPISA
8
C: Outer membrane protein W
D: Outer membrane protein W
E: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3776
Polymers65,1003
Non-polymers2763
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-30 kcal/mol
Surface area23710 Å2
MethodPISA
9
A: Outer membrane protein W
B: Outer membrane protein W
F: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3776
Polymers65,1003
Non-polymers2763
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-29 kcal/mol
Surface area23740 Å2
MethodPISA
10
B: Outer membrane protein W
C: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5844
Polymers43,4002
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-22 kcal/mol
Surface area16880 Å2
MethodPISA
11
A: Outer membrane protein W
hetero molecules

D: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5844
Polymers43,4002
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area1950 Å2
ΔGint-22 kcal/mol
Surface area16890 Å2
MethodPISA
12
E: Outer membrane protein W
hetero molecules

F: Outer membrane protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5844
Polymers43,4002
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area1680 Å2
ΔGint-18 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.666, 118.776, 118.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Outer membrane protein W


Mass: 21700.102 Da / Num. of mol.: 6
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 27-33% MPD, 0.2 M ammonium acetate, 50 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2005
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→37.56 Å / Num. all: 52992 / Num. obs: 52992 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 25.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.25 / Num. unique all: 4351 / % possible all: 82.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASER(CCP4)phasing
CNS1.1refinement
HKL-2000data reduction
CCP4(PHASER)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F1T, MOL_A

2f1t


Resolution: 2.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 3466 -random
Rwork0.292 ---
all0.293 44731 --
obs0.293 44726 100 %-
Displacement parametersBiso mean: 41.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8544 0 36 0 8580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_improper_angle_d0.95
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.369 434 -
Rwork0.336 --
obs-5507 99.8 %

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