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- PDB-3aqp: Crystal structure of SecDF, a translocon-associated membrane prot... -

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Basic information

Entry
Database: PDB / ID: 3aqp
TitleCrystal structure of SecDF, a translocon-associated membrane protein, from Thermus thrmophilus
ComponentsProbable SecDF protein-export membrane protein
KeywordsMEMBRANE PROTEIN / SECDF / SEC / TRANSLOCON / CELL MEMBRANE / MEMBRANE / PROTEIN TRANSPORT / TRANSLOCATION / TRANSMEMBRANE / TRANSPORT
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
Gyrase A; domain 2 - #200 / Alpha-Beta Plaits - #3220 / : / : / Protein translocase subunit SecDF, P1 domain, N-terminal / 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 ...Gyrase A; domain 2 - #200 / Alpha-Beta Plaits - #3220 / : / : / Protein translocase subunit SecDF, P1 domain, N-terminal / 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 / Sterol-sensing domain / Gyrase A; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein translocase subunit SecDF
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsTsukazaki, T. / Mori, H. / Echizen, Y. / Ishitani, R. / Fukai, S. / Tanaka, T. / Perederina, A. / Vassylyev, D.G. / Kohno, T. / Ito, K. / Nureki, O.
CitationJournal: Nature / Year: 2011
Title: Structure and function of a membrane component SecDF that enhances protein export
Authors: Tsukazaki, T. / Mori, H. / Echizen, Y. / Ishitani, R. / Fukai, S. / Tanaka, T. / Perederina, A. / Vassylyev, D.G. / Kohno, T. / Maturana, A.D. / Ito, K. / Nureki, O.
History
DepositionNov 16, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Probable SecDF protein-export membrane protein
B: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)161,1802
Polymers161,1802
Non-polymers00
Water0
1
A: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)80,5901
Polymers80,5901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)80,5901
Polymers80,5901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.636, 140.636, 160.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPVALVALchain A and (resseq 2:515 or resseq 522:726 )AA2 - 5152 - 515
12TYRTYRARGARGchain A and (resseq 2:515 or resseq 522:726 )AA522 - 726522 - 726
21ASPASPVALVALchain B and (resseq 2:515 or resseq 522:726 )BB2 - 5152 - 515
22TYRTYRARGARGchain B and (resseq 2:515 or resseq 522:726 )BB522 - 726522 - 726

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Components

#1: Protein Probable SecDF protein-export membrane protein


Mass: 80589.758 Da / Num. of mol.: 2 / Mutation: N2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: SECDF, TTHA0697 / Plasmid: PTV118N / Production host: Escherichia coli (E. coli) / Strain (production host): AD202 / References: UniProt: Q5SKE6

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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: 4.93 Å3/Da / Density % sol: 75.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 400, 0.2M SODIUM ACETETE, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.501
ReflectionResolution: 3.3→50 Å / Num. obs: 41841

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Processing

Software
NameVersionClassification
MLPHAREphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.3→46.879 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7247 / σ(F): 0.7 / Phase error: 34.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.319 2304 5.51 %
Rwork0.298 --
obs0.2991 41834 88.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso max: 418.65 Å2 / Biso min: 18.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.6946 Å20 Å20 Å2
2---2.6946 Å2-0 Å2
3---5.3891 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11028 0 0 0 11028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511280
X-RAY DIFFRACTIONf_angle_d1.29815244
X-RAY DIFFRACTIONf_dihedral_angle_d18.1114080
X-RAY DIFFRACTIONf_chiral_restr0.0741852
X-RAY DIFFRACTIONf_plane_restr0.0051936
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5514X-RAY DIFFRACTIONPOSITIONAL0.013
12B5514X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.299-3.37550.39231340.34122354X-RAY DIFFRACTION76
3.3755-3.45970.3551270.33372363X-RAY DIFFRACTION76
3.4597-3.55290.32381260.30632379X-RAY DIFFRACTION76
3.5529-3.65710.32841410.30262337X-RAY DIFFRACTION75
3.6571-3.77460.33651340.29512460X-RAY DIFFRACTION79
3.7746-3.90890.34661320.28652516X-RAY DIFFRACTION80
3.9089-4.06460.28391410.27352542X-RAY DIFFRACTION82
4.0646-4.24860.32561600.27652724X-RAY DIFFRACTION87
4.2486-4.4710.25841460.27432761X-RAY DIFFRACTION89
4.471-4.74890.30481440.27262793X-RAY DIFFRACTION89
4.7489-5.1120.29631480.29952878X-RAY DIFFRACTION92
5.112-5.61980.32811430.32442869X-RAY DIFFRACTION92
5.6198-6.41790.37031550.35462929X-RAY DIFFRACTION93
6.4179-8.02970.35911390.30392969X-RAY DIFFRACTION95
8.0297-23.19410.29571570.26912805X-RAY DIFFRACTION88

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