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- PDB-5tgj: Structure of the SNX5 PX domain in complex with chlamydial protei... -

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Basic information

Entry
Database: PDB / ID: 5tgj
TitleStructure of the SNX5 PX domain in complex with chlamydial protein IncE in space group I2
Components
  • IncE
  • Sorting nexin-5
KeywordsPROTEIN TRANSPORT / host-pathogen endosome
Function / homology
Function and homology information


retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / retrograde transport, endosome to Golgi / phagocytic cup / Golgi Associated Vesicle Biogenesis / dynactin binding ...retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / retrograde transport, endosome to Golgi / phagocytic cup / Golgi Associated Vesicle Biogenesis / dynactin binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / ruffle / phosphatidylinositol binding / intracellular protein transport / cytoplasmic side of plasma membrane / endosome / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / membrane / cytosol
Similarity search - Function
Inclusion membrane protein E / Inclusion membrane protein E / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. ...Inclusion membrane protein E / Inclusion membrane protein E / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IncE / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Chlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCollins, B. / Paul, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1061574 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1058734 Australia
Australian Research Council (ARC)DP150100364 Australia
CitationJournal: To Be Published
Title: Structure of the SNX5 PX domain in complex with chlamydial protein IncE
Authors: Collins, B. / Paul, B.
History
DepositionSep 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-5
B: IncE
C: Sorting nexin-5
D: IncE


Theoretical massNumber of molelcules
Total (without water)39,5564
Polymers39,5564
Non-polymers00
Water1,24369
1
A: Sorting nexin-5
B: IncE


Theoretical massNumber of molelcules
Total (without water)19,7782
Polymers19,7782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area9830 Å2
MethodPISA
2
C: Sorting nexin-5
D: IncE


Theoretical massNumber of molelcules
Total (without water)19,7782
Polymers19,7782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.440, 80.320, 94.722
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Sorting nexin-5 /


Mass: 17471.605 Da / Num. of mol.: 2 / Fragment: UNP residues 22-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3
#2: Protein/peptide IncE


Mass: 2306.615 Da / Num. of mol.: 2 / Fragment: UNP residues 111-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: incE / Production host: Escherichia coli (E. coli) / References: UniProt: B7SCI5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M NaCl, 0.1 M MgCl2, 0.1 M Nacitrate (pH 3.5), 12 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→31.9 Å / Num. obs: 13432 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.153 / Net I/σ(I): 39.6
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→31.9 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1345 10.01 %
Rwork0.1991 --
obs0.2035 13432 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 0 69 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112682
X-RAY DIFFRACTIONf_angle_d1.1523625
X-RAY DIFFRACTIONf_dihedral_angle_d17.3951004
X-RAY DIFFRACTIONf_chiral_restr0.074401
X-RAY DIFFRACTIONf_plane_restr0.009469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6930.3321340.27581205X-RAY DIFFRACTION100
2.693-2.80080.35071330.26461199X-RAY DIFFRACTION100
2.8008-2.92820.31251340.26341210X-RAY DIFFRACTION100
2.9282-3.08260.30841350.23521211X-RAY DIFFRACTION100
3.0826-3.27570.27261340.22061204X-RAY DIFFRACTION100
3.2757-3.52850.23381330.2141194X-RAY DIFFRACTION100
3.5285-3.88340.20481350.17221217X-RAY DIFFRACTION100
3.8834-4.4450.20381340.14981210X-RAY DIFFRACTION100
4.445-5.59880.1831340.15511208X-RAY DIFFRACTION100
5.5988-46.91430.23481390.19921240X-RAY DIFFRACTION99

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