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- PDB-5xan: Crystal structure of SecDF in I form (P212121 space group) -

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Basic information

Entry
Database: PDB / ID: 5xan
TitleCrystal structure of SecDF in I form (P212121 space group)
ComponentsProtein translocase subunit SecD
KeywordsMEMBRANE PROTEIN / alfa helical / Sec translocon
Function / homology
Function and homology information


protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein targeting / protein transport / 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 (SSD) profile. / Sterol-sensing domain / Gyrase A; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Multifunctional fusion protein
Similarity search - Component
Biological speciesDeinococcus radiodurans str. R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTsukazaki, T. / Tanaka, Y. / Furukwa, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHIJP26119006, JP26119007, JP26291023, JP16K14713, JP15H01537, 15H05594, JP15J08235, JP15K06972, and JP15K14490 Japan
CitationJournal: Cell Rep / Year: 2017
Title: Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF
Authors: Furukawa, A. / Yoshikaie, K. / Mori, T. / Mori, H. / Morimoto, Y.V. / Sugano, Y. / Iwaki, S. / Minamino, T. / Sugita, Y. / Tanaka, Y. / Tsukazaki, T.
History
DepositionMar 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2May 22, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 14, 2020Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_details
Revision 1.4Nov 11, 2020Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.details
Revision 1.5Feb 9, 2022Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.pdbx_model_details
Revision 1.6Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein translocase subunit SecD
B: Protein translocase subunit SecD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,59415
Polymers161,2662
Non-polymers9,32813
Water2,198122
1
A: Protein translocase subunit SecD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0595
Polymers80,6331
Non-polymers1,4264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein translocase subunit SecD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,53510
Polymers80,6331
Non-polymers7,9029
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.545, 73.814, 369.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein translocase subunit SecD / Protein-export membrane protein SecF


Mass: 80633.000 Da / Num. of mol.: 2 / Fragment: UNP residues 28-768 / Mutation: I117C/L242C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans str. R1 (radioresistant)
Strain: R1 / Gene: secD, secF, DR_1822 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9RTE3
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.6 / Details: 40% PEG 200, 100mM Na-citrate, 100mM LiSO4

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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: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 47548 / % possible obs: 97.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 41.67 Å2 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.059 / Rrim(I) all: 0.154 / Χ2: 1.042 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7550.5550.8130.2610.6170.51386.4
2.75-2.85.30.4990.8720.2330.5530.54496
2.8-2.855.80.4450.9050.1990.4890.57296.8
2.85-2.916.10.4210.9190.1840.4620.61999.2
2.91-2.976.20.3740.9220.1620.4090.65898.9
2.97-3.046.20.330.9280.1440.3620.72199.5
3.04-3.126.30.3040.9420.1310.3320.75299.4
3.12-3.26.30.2680.9620.1150.2920.82899.9
3.2-3.36.40.2450.9610.1040.2670.89599.6
3.3-3.46.40.2240.9640.0950.2440.99299.5
3.4-3.526.50.190.9780.080.2071.10199.6
3.52-3.666.60.1750.9760.0730.191.252100
3.66-3.836.70.1540.9830.0650.1681.30999.5
3.83-4.036.70.1340.9880.0550.1461.46499.8
4.03-4.296.90.1160.990.0470.1261.52799.8
4.29-4.626.10.1110.9910.0470.1211.57782.4
4.62-5.087.20.0960.9950.0380.1031.46399.9
5.08-5.817.20.1040.9940.0410.1121.189100
5.81-7.327.10.0930.9950.0370.11.033100
7.32-506.70.0540.9970.0220.0591.23999.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AQP

3aqp


Resolution: 2.75→48.195 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.2676 1927 4.21 %
Rwork0.2123 --
obs0.2146 45733 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 187.58 Å2 / Biso mean: 47.695 Å2 / Biso min: 10.09 Å2
Refinement stepCycle: final / Resolution: 2.75→48.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11035 0 156 122 11313
Biso mean--45.93 30.59 -
Num. residues----1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111380
X-RAY DIFFRACTIONf_angle_d1.05715424
X-RAY DIFFRACTIONf_chiral_restr0.0541846
X-RAY DIFFRACTIONf_plane_restr0.0071938
X-RAY DIFFRACTIONf_dihedral_angle_d19.6036767
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.81880.31661310.24282985311696
2.8188-2.8950.29321360.2443072320898
2.895-2.98020.31211360.253093322999
2.9802-3.07630.30861380.24213132327099
3.0763-3.18630.31011380.239131393277100
3.1863-3.31380.2461370.231331093246100
3.3138-3.46460.30231370.228731263263100
3.4646-3.64720.24481390.221631543293100
3.6472-3.87560.28281390.21531723311100
3.8756-4.17470.32011390.207131513290100
4.1747-4.59450.22621250.18882849297488
4.5945-5.25860.24731390.1953158329799
5.2586-6.62260.28421440.220932543398100
6.6226-48.20280.20851490.17583412356199
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)
10.75070.9989-0.85021.9609-1.67831.3218-0.39260.3843-0.5604-0.6886-0.00470.04362.1383-1.35650.49531.2647-0.70790.0041.0713-0.10230.4762-42.1628-12.3513-41.4305
28.1024-5.92522.54719.0565-0.73797.00450.09020.1039-0.35490.1107-0.24750.92230.1384-0.91430.12850.2616-0.07120.00180.5007-0.04050.3441-37.26185.697-68.0303
35.58280.8825-0.35754.64740.00454.67350.16890.1465-0.230.1347-0.0724-0.70090.23820.8104-0.01510.2230.0359-0.04620.312-0.04180.3661-37.3970.7803-94.7273
43.21952.48953.56671.84742.39633.90350.2842-0.072-0.20270.13250.1162-0.26090.25520.3888-0.29160.34560.0029-0.00510.4388-0.02410.308-35.7813-0.496-84.1603
51.63490.15220.18011.864-0.26225.72160.0167-0.3259-0.06750.2287-0.06580.07460.8524-0.69790.03240.3681-0.1507-0.0040.35290.0090.2484-32.7364-2.7909-27.7075
61.42410.97140.24970.75310.29781.26010.0807-0.2539-0.26880.2864-0.0852-0.07530.53360.5740.02310.38740.10370.00020.44480.02380.3795-13.6437.3775-32.5073
71.4984-0.2586-0.48961.2690.73136.0506-0.1035-0.0792-0.0362-0.0410.103-0.09280.31790.5014-0.01810.1756-0.0572-0.00130.1852-0.00560.2731-19.317410.7869-45.2852
82.1115-0.5655-0.70713.7321.46467.19610.1461-0.30940.2804-0.11480.2572-0.204-0.77180.5769-0.36340.2515-0.08130.03280.3808-0.0080.2656-18.403510.3221-22.1257
91.8257-1.72852.1623.9456-4.25955.31260.23090.212-0.2436-0.2596-0.4646-0.17570.33740.49390.26730.2775-0.0314-0.02070.2787-0.06610.3355-57.34315.8099-47.1215
105.77472.02561.05883.9535-0.74818.81770.2127-0.2445-0.4204-0.0943-0.1537-0.19750.3776-0.2859-0.03540.2523-0.0050.04340.1318-0.00640.2041-65.934126.1194-69.89
110.51270.11810.64410.22590.29784.53720.00160.0501-0.0715-0.08170.0673-0.0649-0.04830.2948-0.05130.18210.0010.03280.1691-0.00360.2609-58.893423.006-76.5529
121.93160.1584-0.69422.3464-0.19494.07620.0034-0.47820.13540.3622-0.0720.0078-0.0696-0.01720.08920.1807-0.02760.01040.4124-0.00640.2615-58.334527.4705-24.3244
131.24850.1742-2.06640.9075-0.25156.30290.0452-0.25550.06710.0478-0.0554-0.0966-1.00520.5523-0.0650.4515-0.0643-0.09340.3010.02130.3156-57.550547.0125-50.8915
141.7257-0.27150.1331.4841-0.07696.26230.012-0.21620.26690.21360.03190.1021-0.8576-0.6052-0.07720.409-0.04940.0070.34480.01580.2658-61.227543.7127-23.5604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 78 )A30 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 145 )A79 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 236 )A146 - 236
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 288 )A237 - 288
5X-RAY DIFFRACTION5chain 'A' and (resid 289 through 453 )A289 - 453
6X-RAY DIFFRACTION6chain 'A' and (resid 454 through 518 )A454 - 518
7X-RAY DIFFRACTION7chain 'A' and (resid 519 through 680 )A519 - 680
8X-RAY DIFFRACTION8chain 'A' and (resid 681 through 757 )A681 - 757
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 92 )B28 - 92
10X-RAY DIFFRACTION10chain 'B' and (resid 93 through 145 )B93 - 145
11X-RAY DIFFRACTION11chain 'B' and (resid 146 through 344 )B146 - 344
12X-RAY DIFFRACTION12chain 'B' and (resid 345 through 472 )B345 - 472
13X-RAY DIFFRACTION13chain 'B' and (resid 473 through 649 )B473 - 649
14X-RAY DIFFRACTION14chain 'B' and (resid 650 through 760 )B650 - 760

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