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- PDB-3aqo: Structure and function of a membrane component SecDF that enhance... -

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Basic information

Entry
Database: PDB / ID: 3aqo
TitleStructure and function of a membrane component SecDF that enhances protein export
ComponentsProbable SecDF protein-export membrane protein
KeywordsMEMBRANE PROTEIN / PERIPLASMIC DOMAIN / 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
Alpha-Beta Plaits - #3400 / Gyrase A; domain 2 - #200 / : / : / 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 ...Alpha-Beta Plaits - #3400 / Gyrase A; domain 2 - #200 / : / : / 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 / MAD / Resolution: 2.6 Å
AuthorsEchizen, Y. / Tsukazaki, T. / Ishitani, R. / Nureki, O.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus.
Authors: Tsukazaki, T. / Mori, H. / Fukai, S. / Numata, T. / Perederina, A. / Adachi, H. / Matsumura, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Sasaki, T. / Vassylyev, D.G. / Nureki, O. / Ito, K.
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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Probable SecDF protein-export membrane protein
B: Probable SecDF protein-export membrane protein
C: Probable SecDF protein-export membrane protein
D: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)99,2064
Polymers99,2064
Non-polymers00
Water1,72996
1
A: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)24,8011
Polymers24,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)24,8011
Polymers24,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)24,8011
Polymers24,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)24,8011
Polymers24,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.041, 35.829, 181.548
Angle α, β, γ (deg.)90.00, 113.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Probable SecDF protein-export membrane protein


Mass: 24801.479 Da / Num. of mol.: 4 / Fragment: SecDF P1 domain (UNP RESIDUES 35-263)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Gene: secDF, TTHA0697 / Plasmid: PET-26B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SKE6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 3350, 0.6M Sodium thiocyanate, 3% trehalose, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.97942
SYNCHROTRONPhoton Factory AR-NW12A20.97923, 0.97931, 0.98319, 0.96408
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 3, 2007
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979231
30.979311
40.983191
50.964081
ReflectionResolution: 2.6→50 Å / Num. obs: 24792

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→36.86 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 28.174 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1341 5.1 %RANDOM
Rwork0.223 ---
obs0.226 24792 86.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.03 Å2
2---0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6764 0 0 96 6860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0049256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54524.474304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.943151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2961572
X-RAY DIFFRACTIONr_chiral_restr0.0810.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4461.54396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85527100
X-RAY DIFFRACTIONr_scbond_it1.28232436
X-RAY DIFFRACTIONr_scangle_it2.2994.52156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 64 -
Rwork0.259 1344 -
obs--64.77 %
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)
14.5636-0.57752.43842.5015-0.10846.16020.21640.2983-0.2446-0.1190.0690.12140.5905-0.1483-0.28540.1914-0.0908-0.0470.08460.00440.026417.39761.0338-30.1869
21.3598-0.23160.56832.36360.03321.2336-0.0285-0.0033-0.0208-0.11490.02060.1467-0.0235-0.05320.00790.0755-0.02530.00180.0690.00650.073225.26289.1083-6.543
34.3023-0.27672.73082.95510.11226.33910.0559-0.1873-0.17820.12410.0810.0610.08810.0009-0.13690.08560.033-0.02440.04310.01060.0235-61.3424-8.0499-52.9603
41.26780.11120.2522.47030.12031.27290.0256-0.0579-0.05560.0938-0.0058-0.1426-0.03710.0605-0.01980.06860.0222-0.00780.06620.00240.0737-69.306-0.1868-76.6188
59.93143.3525-1.66385.42273.09177.80590.03050.76810.15570.13510.184-0.2750.1756-0.1889-0.21450.0582-0.08650.00310.20220.00050.0314-6.86648.2516-37.1362
61.5204-0.00810.43573.1691-0.90682.0264-0.20850.0947-0.0099-0.29020.3482-0.12560.13090.0124-0.13970.0815-0.06180.01690.1272-0.01540.0466-21.6706-0.297-17.7159
78.0759-1.72550.62955.9503-3.17288.24770.2619-0.32930.0868-0.2477-0.32620.15280.27590.09830.06430.0633-0.00210.03990.0455-0.02130.0447-37.1139-1.3767-45.9904
81.0411-0.13960.34172.70011.37352.3593-0.1886-0.07540.00830.33810.34210.23870.22930.1418-0.15350.09080.06770.00890.13050.03030.0785-22.3666-9.6965-65.4732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 110
2X-RAY DIFFRACTION1A250 - 262
3X-RAY DIFFRACTION2A111 - 249
4X-RAY DIFFRACTION3B43 - 110
5X-RAY DIFFRACTION3B250 - 262
6X-RAY DIFFRACTION4B111 - 249
7X-RAY DIFFRACTION5C41 - 110
8X-RAY DIFFRACTION5C250 - 262
9X-RAY DIFFRACTION6C111 - 249
10X-RAY DIFFRACTION7D42 - 110
11X-RAY DIFFRACTION7D250 - 262
12X-RAY DIFFRACTION8D111 - 249

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