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- PDB-5yhf: Crystal structure of SecDF in Super-membrane-facing form -

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Basic information

Entry
Database: PDB / ID: 5yhf
TitleCrystal structure of SecDF in Super-membrane-facing form
ComponentsProtein translocase subunit SecDF
KeywordsMEMBRANE PROTEIN / beta barrel / TRANSPORT PROTEIN / MOTOR PROTEIN
Function / homology
Function and homology information


protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein targeting / plasma membrane
Similarity search - Function
Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / : / : / : / Protein export membrane protein / SecD/SecF GG Motif ...Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / : / : / : / Protein export membrane protein / SecD/SecF GG Motif / Protein translocase subunit SecDF, P1 domain, N-terminal / SecDF, P1 head subdomain / Sterol-sensing domain
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Protein translocase subunit SecDF
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Yoshikaie, K. / Furukawa, A.
Funding support Japan, 5items
OrganizationGrant numberCountry
JSPS/MEXT KAKENHIJP26119007, JP26291023, JP17H05669, JP16K14713, JP15H01537, JP15J08235, 15K14490, JP15K06972 Japan
Mitsubishi Foundation Japan
Noguchi Institute Japan
Naito Foundation Japan
Mochida Memorial Foundation for Medical and Pharmaceutical Research Japan
CitationJournal: Structure / Year: 2018
Title: Remote Coupled Drastic beta-Barrel to beta-Sheet Transition of the Protein Translocation Motor.
Authors: Furukawa, A. / Nakayama, S. / Yoshikaie, K. / Tanaka, Y. / Tsukazaki, T.
History
DepositionSep 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Structure summary / Category: citation / struct
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Protein translocase subunit SecDF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4797
Polymers80,5901
Non-polymers1,8896
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint3 kcal/mol
Surface area33230 Å2
Unit cell
Length a, b, c (Å)55.190, 65.640, 79.980
Angle α, β, γ (deg.)75.110, 75.230, 80.830
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein translocase subunit SecDF


Mass: 80589.758 Da / Num. of mol.: 1 / Mutation: N2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: secDF, TTHA0697 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q5SKE6
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 8.5 / Details: 50% PEG 400, 100 mM Tris-HCl pH 8.5, 100 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.864 Å / Num. obs: 25694 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 23 % / Biso Wilson estimate: 44.24 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.0656 / Rrim(I) all: 0.671 / Χ2: 1.13 / Net I/σ(I): 8.23 / Num. measured all: 590974 / Scaling rejects: 2022
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.9722.610.90481.8194192416441660.7899.251100
2.97-3.1722.8024.2552.686899381438110.8534.35199.9
3.17-3.4323.0681.724.2186760377637610.9091.75899.6
3.43-3.7621.9910.9356.673098332533240.9550.957100
3.76-4.223.4930.52610.0671089303030260.9760.53799.9
4.2-4.8523.9860.33514.2763684265526550.9860.343100
4.85-5.9323.4970.29614.1252681224622420.9860.30299.8
5.93-8.3721.9460.22217.1738471176517530.9920.22799.3
8.37-48.86425.2090.1427.48241009629560.9950.14299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
MoRDaphasing
PDB_EXTRACT3.22data extraction
XDSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AQP

3aqp


Resolution: 2.8→48.864 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1999 7.79 %
Rwork0.2034 23678 -
obs0.2067 25677 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.8 Å2 / Biso mean: 47.235 Å2 / Biso min: 1.23 Å2
Refinement stepCycle: final / Resolution: 2.8→48.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 132 27 5779
Biso mean--75.07 38.49 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025854
X-RAY DIFFRACTIONf_angle_d0.4557916
X-RAY DIFFRACTIONf_chiral_restr0.036948
X-RAY DIFFRACTIONf_plane_restr0.0031002
X-RAY DIFFRACTIONf_dihedral_angle_d7.5654853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.870.36631430.289716911834
2.87-2.94760.30821410.264416721813
2.9476-3.03440.30461440.252417111855
3.0344-3.13230.3081440.236516991843
3.1323-3.24420.2761420.226816951837
3.2442-3.37410.27711400.22716601800
3.3741-3.52760.28811450.229717061851
3.5276-3.71350.26191430.210517061849
3.7135-3.94610.23881440.184216981842
3.9461-4.25060.22391420.187816801822
4.2506-4.6780.23231420.176816901832
4.678-5.35420.20471430.179516941837
5.3542-6.7430.25961430.214116861829
6.743-48.87150.16571430.160916901833
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8997-0.1891-0.45020.28770.07330.21230.09790.28580.01660.024-0.12320.0895-0.2752-0.3537-0.09270.39060.11430.02520.18170.03260.1712-4.782916.6914-17.5421
20.39580.15860.07330.8102-0.24150.28920.0212-0.0094-0.0438-0.1506-0.1023-0.0741-0.0734-0.0881-0.00030.2690.0882-0.01370.2036-0.00010.266916.902316.7974-38.5461
30.21280.0777-0.0110.4009-0.28310.4243-0.01270.02520.09760.1145-0.0392-0.14420.00770.0554-0.05260.20660.1125-0.00940.27270.03950.300523.538216.7687-37.0146
40.7584-0.08280.18520.5170.05470.68540.0062-0.05820.03470.04310.0028-0.0035-0.2252-0.12340.00310.1721-0.04170.02280.1907-0.01760.1863-4.75828.89552.4535
50.1641-0.09230.18110.2281-0.08880.2420.25740.2113-0.17890.0485-0.29310.07730.13-0.3153-0.01090.39140.0036-0.00680.278-0.02450.29581.8926-10.971110.0855
60.25670.15940.32950.18080.1460.37560.13730.0958-0.081-0.1207-0.0653-0.0586-0.0708-0.03850.00120.21340.0518-0.00080.3378-0.01580.1522-2.9634-8.5023-28.3116
70.315-0.1870.11890.101-0.0540.1727-0.007-0.0318-0.0120.0605-0.04270.00750.19320.0548-00.2589-0.01-0.00320.1824-0.0080.18696.0302-6.84655.0085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 55 )A2 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 185 )A56 - 185
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 267 )A186 - 267
4X-RAY DIFFRACTION4chain 'A' and (resid 268 through 427 )A268 - 427
5X-RAY DIFFRACTION5chain 'A' and (resid 428 through 469 )A428 - 469
6X-RAY DIFFRACTION6chain 'A' and (resid 470 through 588 )A470 - 588
7X-RAY DIFFRACTION7chain 'A' and (resid 589 through 735 )A589 - 735

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