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- PDB-5xam: Crystal structure of SecDF in I form at 4 A resolution -

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Basic information

Entry
Database: PDB / ID: 5xam
TitleCrystal structure of SecDF in I form at 4 A resolution
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
Multifunctional fusion protein
Similarity search - Component
Biological speciesDeinococcus radiodurans str. R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsTsukazaki, T. / Tanaka, Y. / Furukwa, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHIJP26119006, JP26119007, JP26291023, JP16K14713, JP15H01537, 15H05594, JP15J08235, JP15K06972, 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 / diffrn_radiation
Item: _diffrn_detector.details / _diffrn_radiation.monochromator
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


Theoretical massNumber of molelcules
Total (without water)161,3062
Polymers161,3062
Non-polymers00
Water0
1
A: Protein translocase subunit SecD


Theoretical massNumber of molelcules
Total (without water)80,6531
Polymers80,6531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein translocase subunit SecD


Theoretical massNumber of molelcules
Total (without water)80,6531
Polymers80,6531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.320, 62.260, 181.710
Angle α, β, γ (deg.)90.000, 101.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 80653.031 Da / Num. of mol.: 2 / Fragment: UNP residues 28-768
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

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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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6 / Details: 38% PEG 200, NH4-citrate

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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: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 17534 / % possible obs: 36 % / Redundancy: 2.5 % / Biso Wilson estimate: 149.47 Å2 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.111 / Rrim(I) all: 0.186 / Χ2: 1.301 / Net I/σ(I): 2.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
4-4.072.10.8210.3790.6250.49114.5
4.07-4.142.20.7250.5270.5030.62814.90.887
4.14-4.222.40.3620.8150.60115
4.22-4.312.40.9020.6920.6310.58617.2
4.31-4.42.40.5220.7050.3620.71117.90.639
4.4-4.52.50.4360.5260.3050.8819.30.535
4.5-4.622.50.6230.7740.4230.73718.40.757
4.62-4.742.50.5520.7380.3760.56320.10.671
4.74-4.882.50.3220.9120.2210.833200.393
4.88-5.042.50.2850.9330.1940.78222.60.347
5.04-5.222.50.2950.880.1950.8923.50.355
5.22-5.432.50.2720.950.1820.66626.60.329
5.43-5.672.30.420.8520.2860.59337.10.511
5.67-5.972.30.6150.7150.4380.53849.40.759
5.97-6.352.50.640.8030.4370.53162.80.779
6.35-6.842.70.4350.8970.2860.60467.50.523
6.84-7.522.70.2960.9650.20.64767.70.359
7.52-8.62.70.1550.9810.1040.75967.30.188
8.6-10.822.70.0970.9840.0671.28766.90.119
10.82-502.60.0750.990.0556.31164.40.094

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3aqp


Resolution: 4→47.985 Å / SU ML: 1.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 51.95
RfactorNum. reflection% reflection
Rfree0.402 1711 10 %
Rwork0.3326 --
obs0.3395 17102 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 449.7 Å2 / Biso mean: 242.314 Å2 / Biso min: 52.04 Å2
Refinement stepCycle: final / Resolution: 4→47.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9852 0 0 0 9852
Num. residues----1411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039997
X-RAY DIFFRACTIONf_angle_d0.70813699
X-RAY DIFFRACTIONf_chiral_restr0.0421789
X-RAY DIFFRACTIONf_plane_restr0.0061716
X-RAY DIFFRACTIONf_dihedral_angle_d13.2355864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4-4.11770.48851380.3741250138896
4.1177-4.25050.44111230.39471247137094
4.2505-4.40230.51541500.46981187133792
4.4023-4.57840.57511120.49771047115979
4.5784-4.78660.50161520.450513321484100
4.7866-5.03870.46911380.41241290142899
5.0387-5.35410.43361510.391313081459100
5.3541-5.76680.39761390.405713331472100
5.7668-6.3460.44031480.414113301478100
6.346-7.26150.43591530.397213271480100
7.2615-9.13840.39731540.300413431497100
9.1384-47.98880.29741530.20951397155099
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)
12.32961.1335-1.94383.33163.25837.90680.1157-0.93380.66-0.8355-0.0189-1.2986-0.96361.442-0.18720.45160.31370.41931.8819-0.05372.4495-11.63963.647738.6215
23.69031.24020.48693.3544-1.27076.7738-0.18751.27230.7421-1.0797-0.0457-0.62211.59621.62190.09871.54790.09550.44831.62170.21611.9013-5.4274-6.8130.7564
32.8852-2.7895-1.61721.8466-0.83199.1516-0.312-0.3039-1.3220.274-0.0745-0.4201-0.1438-0.60380.44430.60510.0757-0.07991.0826-0.40251.5462-20.2531-6.319951.6767
41.1577-1.93582.2623.6398-2.46182.572-0.84980.4442-1.01640.90230.0107-0.53211.02890.8749-0.33430.07640.1164-0.13221.5819-0.20812.0871-16.5653-13.490860.7545
53.514-0.4992-4.87553.4636-2.36819.71121.75421.0961-0.09760.29681.3205-0.05182.65831.52632.1821.3499-1.8275-1.54443.2236-2.08921.3629-28.3254-28.134225.6804
60.10430.8629-1.094.0617-0.81236.7176-0.99171.2997-1.63620.346-0.8191-0.51921.02651.44440.24490.70660.4343-0.33722.6762-0.65921.9503-12.1809-22.921542.2291
72.06120.45810.13844.96132.26867.6484-0.2930.33040.69841.2636-0.5451-0.69752.41760.7784-0.84190.7543-0.1158-0.13761.37470.06421.4439-16.1253-22.890365.424
87.6257-3.3274-2.28712.0227-0.18116.87181.58541.73540.763-4.5341-1.5349-1.3992-0.5244-0.2550.55572.0996-1.81231.0476-0.46970.2792.468623.4046-1.180949.9323
94.2246-0.9947-2.87443.9555-0.26732.48160.83520.22810.5796-2.9394-1.4098-4.4347-0.68620.5172-0.41063.12991.47632.94191.2994-0.72292.271636.5301-18.697324.7963
104.60860.89591.01132.1819-0.19310.402-1.16670.6198-0.7662-1.3416-0.2715-0.7225-0.70591.81940.10811.12470.22260.6512.05890.92323.093831.3433-23.32975.1684
112.4329-0.5195-0.83569.80396.10797.094-0.05612.27911.3776-0.57391.5743-1.1667-1.76493.00381.7672.6340.6187-0.70744.76391.58982.154237.8156-14.592-6.4467
121.14492.23291.11274.51032.15021.0323-2.55750.42970.9859-0.94710.30350.46561.76880.70140.1442.33241.64731.414.63030.95532.716132.7109-21.95717.9904
135.0488-2.17350.63355.1812-3.63814.5421-1.1424-0.42840.44721.68230.0319-0.8407-0.4303-0.91260.58131.5789-0.09970.26790.6969-0.73360.953622.9785-18.960261.7711
142.43-0.0441.97553.5433-3.44633.9610.59590.6761-0.15360.2243-1.43620.2150.604-1.54320.29951.1597-0.41610.03150.8055-0.27471.231925.1789-30.461857.0263
152.1468-1.0466-2.60982.37322.4723.8637-0.5003-0.9025-0.61081.9475-0.4168-0.12741.61110.9619-2.85142.5402-0.417-1.09951.75741.09051.245819.1972-40.108123.9586
168.11410.63865.78881.53560.98584.11360.11471.49370.3985-1.90750.21660.95220.11190.5260.3207-1.7083-0.83520.51623.72510.59781.032333.179-33.688538.8827
174.61570.72850.18025.9734-0.1253.69090.288-0.3323-0.59180.5984-0.0610.39330.76011.5502-0.45150.5330.4631-0.24460.83780.04971.00729.0209-36.610164.0466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 110 )A29 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 270 )A111 - 270
3X-RAY DIFFRACTION3chain 'A' and (resid 271 through 380 )A271 - 380
4X-RAY DIFFRACTION4chain 'A' and (resid 381 through 513 )A381 - 513
5X-RAY DIFFRACTION5chain 'A' and (resid 514 through 548 )A514 - 548
6X-RAY DIFFRACTION6chain 'A' and (resid 549 through 644 )A549 - 644
7X-RAY DIFFRACTION7chain 'A' and (resid 645 through 758 )A645 - 758
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 69 )B31 - 69
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 128 )B70 - 128
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 164 )B129 - 164
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 230 )B165 - 230
12X-RAY DIFFRACTION12chain 'B' and (resid 231 through 288 )B231 - 288
13X-RAY DIFFRACTION13chain 'B' and (resid 289 through 408 )B289 - 408
14X-RAY DIFFRACTION14chain 'B' and (resid 409 through 520 )B409 - 520
15X-RAY DIFFRACTION15chain 'B' and (resid 521 through 569 )B521 - 569
16X-RAY DIFFRACTION16chain 'B' and (resid 570 through 617 )B570 - 617
17X-RAY DIFFRACTION17chain 'B' and (resid 618 through 754 )B618 - 754

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