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- PDB-2f1c: Crystal structure of the monomeric porin OmpG -

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Basic information

Entry
Database: PDB / ID: 2f1c
TitleCrystal structure of the monomeric porin OmpG
ComponentsOuter membrane protein G
KeywordsMEMBRANE PROTEIN / beta barrel
Function / homology
Function and homology information


carbohydrate transmembrane transport / oligosaccharide transporting porin activity / maltose transporting porin activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane porin G / Outer membrane protein G (OmpG) / monomeric porin ompg / : / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin G
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSubbarao, G.V. / van den Berg, B.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the Monomeric Porin OmpG.
Authors: Subbarao, G.V. / van den Berg, B.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
X: Outer membrane protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2473
Polymers33,6341
Non-polymers6132
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Outer membrane protein G
hetero molecules

X: Outer membrane protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4946
Polymers67,2682
Non-polymers1,2264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3340 Å2
ΔGint-23 kcal/mol
Surface area28020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.640, 70.142, 59.501
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer membrane protein G / OMPG


Mass: 33634.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species: coli / Strain: K-12 / Gene: ompG / Plasmid: pB22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: P76045
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 28-32% PEG400, 1-1.5 M sodium formate, 50 mM cacodylate pH 5.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2005
RadiationMonochromator: Si(111) channel cut monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→29 Å / Num. all: 20082 / Num. obs: 19961 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.8 / Redundancy: 6.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 25.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1939 / % possible all: 96.6

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Processing

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

Resolution: 2.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 898 random
Rwork0.233 --
all0.237 17541 -
obs0.237 17507 -
Displacement parametersBiso mean: 33.04 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å20 Å21.32 Å2
2--1.12 Å20 Å2
3---2.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 42 113 2255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_improper_angle_d0.74
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.036
RfactorNum. reflection% reflection
Rfree0.338 86 -
Rwork0.269 --
obs-2128 98.4 %

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