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- PDB-2zld: Structure of OmpF co-crystallized with T83 -

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Basic information

Entry
Database: PDB / ID: 2zld
TitleStructure of OmpF co-crystallized with T83
Components
  • Colicin-E3
  • Outer membrane protein F
KeywordsMEMBRANE PROTEIN / BtuB / colicin E3 / ribosomal RNAase / disordered T83 / Tol system / Ion transport / Membrane / Outer membrane / Phage recognition / Porin / Transmembrane / Transport
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / lipid binding / identical protein binding / membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCramer, W.A. / Zakharov, S.D. / Yamashita, E.
CitationJournal: Embo J. / Year: 2008
Title: Crystal structures of the OmpF porin: function in a colicin translocon.
Authors: Yamashita, E. / Zhalnina, M.V. / Zakharov, S.D. / Sharma, O. / Cramer, W.A.
History
DepositionApr 9, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein F
B: Outer membrane protein F
C: Colicin-E3
D: Colicin-E3


Theoretical massNumber of molelcules
Total (without water)75,4564
Polymers75,4564
Non-polymers00
Water00
1
A: Outer membrane protein F
C: Colicin-E3

A: Outer membrane protein F
C: Colicin-E3

A: Outer membrane protein F
C: Colicin-E3


Theoretical massNumber of molelcules
Total (without water)113,1846
Polymers113,1846
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8870 Å2
ΔGint-55 kcal/mol
Surface area41130 Å2
MethodPISA
2
B: Outer membrane protein F
D: Colicin-E3

B: Outer membrane protein F
D: Colicin-E3

B: Outer membrane protein F
D: Colicin-E3


Theoretical massNumber of molelcules
Total (without water)113,1846
Polymers113,1846
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8890 Å2
ΔGint-55 kcal/mol
Surface area41090 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-16 kcal/mol
Surface area32100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.867, 116.867, 114.331
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 1 - 340 / Label seq-ID: 1 - 340

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Outer membrane protein F / Porin ompF / Outer membrane protein 1A / Outer membrane protein IA / Outer membrane protein B


Mass: 37114.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#2: Protein/peptide Colicin-E3 / Colicin-E3 A chain / Ribonuclease


Mass: 613.749 Da / Num. of mol.: 2 / Fragment: T83 (RESIDUES 1-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: Hydrolases; Acting on ester bonds
Sequence detailsTHE AUTHOR CO-CRYSTALLIZED THE OMPF WITH THE N-TERMINAL TRANSLOCATION DOMAIN OF COLICIN E3 (T83). ...THE AUTHOR CO-CRYSTALLIZED THE OMPF WITH THE N-TERMINAL TRANSLOCATION DOMAIN OF COLICIN E3 (T83). THE ELECTRON DENSITY RESEMBLED THAT OF A POLYPEPTIDE CHAIN CONSISTING AT LEAST SEVEN RESIDUES. BUT THE AUTHOR COULDN'T IDENTIFY SPECIFIC REGION OF T83 BECAUSE OF THE LACK OF THE ELECTRON DENSITY. THEREFORE THE SEQUENCE NUMBER IN THE PEPTIDE COORDINATES IS NOT ACTUAL NUMBER. THE SEQUENCE OF THE N-TERMINAL TRANSLOCATION DOMAIN OF T83 IS MSGGDGRGHN TGAHSTSGNI NGGPTGLGVG GGASDGSGWS SENNPWGGGS GSGIHWGGGS GHGNGGGNGN SGGGSGTGGN LSA. THIS SEQUENCE IS DESCRIBED AS THE RESIDUES 1-83 IN THE UNIPROT P00646, CEA3_ECOLX.

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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: 2.99 Å3/Da / Density % sol: 58.82 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 17885 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF

2omf


Resolution: 3→101.02 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.857 / SU B: 23.547 / SU ML: 0.438 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29392 896 5 %RANDOM
Rwork0.26555 ---
obs0.26697 16925 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.67 Å2
Baniso -1Baniso -2Baniso -3
1--5.38 Å2-2.69 Å20 Å2
2---5.38 Å20 Å2
3---8.07 Å2
Refinement stepCycle: LAST / Resolution: 3→101.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5294 0 0 0 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225402
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.9327296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4545686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32324.966290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30915798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.9071522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024340
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.22082
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23635
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.41.53427
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72925270
X-RAY DIFFRACTIONr_scbond_it0.47132292
X-RAY DIFFRACTIONr_scangle_it0.7484.52026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2619 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.010.05
tight thermal0.050.5
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 63 -
Rwork0.322 1259 -
obs--100 %

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