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- PDB-5i97: Structural analysis and inhibition of TraE from the pKM101 type I... -

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Basic information

Entry
Database: PDB / ID: 5i97
TitleStructural analysis and inhibition of TraE from the pKM101 type IV secretion system
ComponentsConjugal transfer protein
KeywordsPROTEIN TRANSPORT / bacterial secretion / type IV secretion / VirB
Function / homology
Function and homology information


protein secretion by the type IV secretion system / membrane
Similarity search - Function
VirB8 protein / Type IV secretion system protein VirB8/PtlE / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Conjugal transfer protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.441 Å
AuthorsCasu, B. / Sygusch, J. / Baron, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR MOP-84239 Canada
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Analysis and Inhibition of TraE from the pKM101 Type IV Secretion System.
Authors: Casu, B. / Smart, J. / Hancock, M.A. / Smith, M. / Sygusch, J. / Baron, C.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conjugal transfer protein
B: Conjugal transfer protein
C: Conjugal transfer protein
D: Conjugal transfer protein


Theoretical massNumber of molelcules
Total (without water)75,2724
Polymers75,2724
Non-polymers00
Water1,20767
1
A: Conjugal transfer protein
B: Conjugal transfer protein


Theoretical massNumber of molelcules
Total (without water)37,6362
Polymers37,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Conjugal transfer protein
D: Conjugal transfer protein


Theoretical massNumber of molelcules
Total (without water)37,6362
Polymers37,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.049, 123.362, 109.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Conjugal transfer protein / Conjugal transfer protein TraE / TraE / TraE protein / Inner membrane protein forms channel for ...Conjugal transfer protein TraE / TraE / TraE protein / Inner membrane protein forms channel for type IV secretion of T-DNA complex / VirB8 / Type IV secretion of T-DNA VirB8 / Uncharacterized protein


Mass: 18818.104 Da / Num. of mol.: 4 / Fragment: residues 42-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: traE, B634_00049, ECONIH1_27615, pec386IL_00125, pEcNDM0_00049, pHKU1_33, pKC394-028, pKC396-021, pMUR050_041, pN3_023, PU53_15805
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q17U16
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 16% (w/v) PEG 10,000, 50 mM Bis-Tris (pH 5.5), 100 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.441→38.6 Å / Num. obs: 28596 / % possible obs: 99.98 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 32.7
Reflection shellResolution: 2.441→2.529 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CC3

2cc3


Resolution: 2.441→38.6 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.86
RfactorNum. reflection% reflection
Rfree0.28 1926 6.98 %
Rwork0.24 --
obs0.2466 27606 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.441→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 0 67 4636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074673
X-RAY DIFFRACTIONf_angle_d1.0916336
X-RAY DIFFRACTIONf_dihedral_angle_d14.1381744
X-RAY DIFFRACTIONf_chiral_restr0.048682
X-RAY DIFFRACTIONf_plane_restr0.007821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4414-2.50240.34531230.30851657X-RAY DIFFRACTION88
2.5024-2.57010.33131290.30331688X-RAY DIFFRACTION91
2.5701-2.64570.3611290.3071737X-RAY DIFFRACTION93
2.6457-2.7310.34131340.30171774X-RAY DIFFRACTION94
2.731-2.82860.33871300.30121784X-RAY DIFFRACTION95
2.8286-2.94180.32131390.30061822X-RAY DIFFRACTION96
2.9418-3.07570.35751360.28441850X-RAY DIFFRACTION98
3.0757-3.23770.32241390.31151843X-RAY DIFFRACTION98
3.2377-3.44050.32531420.28551896X-RAY DIFFRACTION99
3.4405-3.70590.31061410.25851867X-RAY DIFFRACTION100
3.7059-4.07850.29971420.24381895X-RAY DIFFRACTION100
4.0785-4.66780.24281450.19121922X-RAY DIFFRACTION100
4.6678-5.87760.22761460.19611939X-RAY DIFFRACTION100
5.8776-38.6080.21661510.20152006X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -34.266 Å / Origin y: -19.8622 Å / Origin z: -10.2076 Å
111213212223313233
T0.3033 Å20.0195 Å2-0.0924 Å2-0.2966 Å2-0.0585 Å2--0.296 Å2
L1.1136 °20.0264 °2-0.3494 °2-0.5977 °20.1027 °2--0.9673 °2
S0.0619 Å °0.297 Å °-0.0892 Å °-0.047 Å °-0.0288 Å °0.0953 Å °0.1127 Å °-0.1197 Å °-0.0009 Å °
Refinement TLS groupSelection details: all

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