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- PDB-5l0w: Structure of post-translational translocation Sec71/Sec72 complex -

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Basic information

Entry
Database: PDB / ID: 5l0w
TitleStructure of post-translational translocation Sec71/Sec72 complex
Components
  • Sec71
  • Sec72
KeywordsMEMBRANE PROTEIN / protein translocation / TPR domain
Function / homology
Function and homology information


Sec62/Sec63 complex / post-translational protein targeting to membrane, translocation / membrane => GO:0016020
Similarity search - Function
Translocation protein Sec66 / Preprotein translocase subunit Sec66 / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Translocation protein (Sec66)-like protein / Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.035 Å
AuthorsTripathi, A. / Rapoport, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Two alternative binding mechanisms connect the protein translocation Sec71-Sec72 complex with heat shock proteins.
Authors: Tripathi, A. / Mandon, E.C. / Gilmore, R. / Rapoport, T.A.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sec72
A: Sec71


Theoretical massNumber of molelcules
Total (without water)45,4452
Polymers45,4452
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-34 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.600, 108.600, 271.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Sec72


Mass: 24074.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0SH41
#2: Protein Sec71 / Translocation protein (Sec66)-like protein


Mass: 21369.971 Da / Num. of mol.: 1 / Fragment: UNP residues 48-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0B5

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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: 5.44 Å3/Da / Density % sol: 77.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.4M ammonium tatrate dibasic, 0.1M Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.035→20.1 Å / Num. obs: 18882 / % possible obs: 99.8 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 17
Reflection shellResolution: 3.035→3.13 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.7 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.035→20.1 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.76 / Phase error: 28.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2502 1703 4.98 %
Rwork0.2228 32465 -
obs0.2242 34168 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.32 Å2 / Biso mean: 90.0117 Å2 / Biso min: 33.31 Å2
Refinement stepCycle: final / Resolution: 3.035→20.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 0 0 2962
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053017
X-RAY DIFFRACTIONf_angle_d0.9114073
X-RAY DIFFRACTIONf_chiral_restr0.034438
X-RAY DIFFRACTIONf_plane_restr0.004539
X-RAY DIFFRACTIONf_dihedral_angle_d15.2491170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0353-3.12430.33681270.37962441256890
3.1243-3.22470.30941440.33727192863100
3.2247-3.33950.31441500.32427282878100
3.3395-3.47250.3531460.317727412887100
3.4725-3.62970.34891330.283127472880100
3.6297-3.81980.30021390.25527032842100
3.8198-4.05730.24711460.226927362882100
4.0573-4.36760.24751410.205527452886100
4.3676-4.80170.22141460.195227142860100
4.8017-5.48420.29271430.211927282871100
5.4842-6.86350.2421430.21127282871100
6.8635-20.10040.16651450.156627352880100

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