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- PDB-4g7x: Crystal structure of a complex between the CTXphi pIII N-terminal... -

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Basic information

Entry
Database: PDB / ID: 4g7x
TitleCrystal structure of a complex between the CTXphi pIII N-terminal domain and the Vibrio cholerae TolA C-terminal domain
Components
  • Putative uncharacterized protein
  • TolA protein
KeywordsPROTEIN BINDING/PROTEIN BINDING / Membrane / PROTEIN BINDING-PROTEIN BINDING complex
Function / homology
Function and homology information


bacteriocin transport / toxin transmembrane transporter activity / membrane => GO:0016020 / membrane
Similarity search - Function
Vibrio phage CTXphi pIII, N-terminal N1 domain / TolA C-terminal / Tol-Pal system, TolA / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TolA protein / TolA protein / :
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKolappan, S. / Ford, C.G. / Craig, L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structures of a CTX{varphi} pIII Domain Unbound and in Complex with a Vibrio cholerae TolA Domain Reveal Novel Interaction Interfaces.
Authors: Ford, C.G. / Kolappan, S. / Phan, H.T. / Waldor, M.K. / Winther-Larsen, H.C. / Craig, L.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: TolA protein


Theoretical massNumber of molelcules
Total (without water)26,5832
Polymers26,5832
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.380, 46.160, 101.630
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 Putative uncharacterized protein


Mass: 11509.833 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: CIRS101 / Gene: orfU, VCH_002198 / Production host: Escherichia coli (E. coli) / References: UniProt: C6RZG1
#2: Protein TolA protein


Mass: 15072.992 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: tolA, VC0395_A1430, VC395_1952 / Production host: Escherichia coli (E. coli) / References: UniProt: A5F754, UniProt: A0A0H3AIH3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25 % PEG 6000, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 13, 2011 / Details: mirrors
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→39.9 Å / Num. all: 37355 / Num. obs: 35426 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.4 / Redundancy: 6.9 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.042 / Net I/σ(I): 27.3
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 257179 / Rsym value: 0.329 / % possible all: 95.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→39.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.114 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.078 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1865 5 %RANDOM
Rwork0.206 ---
obs0.206 35426 99.66 %-
all-37355 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.936 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.44→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 0 197 1681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191711
X-RAY DIFFRACTIONr_angle_refined_deg0.9741.9832354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0865232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14324.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74315287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.841511
X-RAY DIFFRACTIONr_chiral_restr0.0590.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211357
LS refinement shellResolution: 1.44→1.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 125 -
Rwork0.227 2257 -
obs--95.2 %

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