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Basic information

Entry
Database: PDB / ID: 5xw7
TitleCrystal structure of the flexible tandem repeat domain of bacterial cellulose synthase subunit C
ComponentsCellulose synthase subunit C
KeywordsBIOSYNTHETIC PROTEIN / cellulose synthase / tetratrico peptide repeat
Function / homology
Function and homology information


cellulose biosynthetic process / outer membrane
Similarity search - Function
Cellulose synthase operon C, C-terminal / Cellulose synthase operon protein C C-terminus (BCSC_C) / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Cellulose synthase subunit C
Similarity search - Component
Biological speciesEnterobacter sp. CJF-002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.272 Å
AuthorsNojima, S. / Kato, K. / Yao, M.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of the flexible tandem repeat domain of bacterial cellulose synthesis subunit C.
Authors: Shingo Nojima / Ayumi Fujishima / Koji Kato / Kayoko Ohuchi / Nobutaka Shimizu / Kento Yonezawa / Kenji Tajima / Min Yao /
Abstract: Bacterial cellulose (BC) is synthesized and exported through the cell membrane via a large protein complex (terminal complex) that consists of three or four subunits. BcsC is a little-studied subunit ...Bacterial cellulose (BC) is synthesized and exported through the cell membrane via a large protein complex (terminal complex) that consists of three or four subunits. BcsC is a little-studied subunit considered to export BC to the extracellular matrix. It is predicted to have two domains: a tetratrico peptide repeat (TPR) domain and a β-barrelled outer membrane domain. Here we report the crystal structure of the N-terminal part of BcsC-TPR domain (Asp24-Arg272) derived from Enterobacter CJF-002. Unlike most TPR-containing proteins which have continuous TPR motifs, this structure has an extra α-helix between two clusters of TPR motifs. Five independent molecules in the crystal had three different conformations that varied at the hinge of the inserted α-helix. Such structural feature indicates that the inserted α-helix confers flexibility to the chain and changes the direction of the TPR super-helix, which was also suggested by structural analysis of BcsC-TPR (Asp24-Leu664) in solution by size exclusion chromatography-small-angle X-ray scattering. The flexibility at the α-helical hinge may play important role for exporting glucan chains.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

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Assembly

Deposited unit
A: Cellulose synthase subunit C
B: Cellulose synthase subunit C
C: Cellulose synthase subunit C
D: Cellulose synthase subunit C
E: Cellulose synthase subunit C


Theoretical massNumber of molelcules
Total (without water)142,7705
Polymers142,7705
Non-polymers00
Water00
1
A: Cellulose synthase subunit C


Theoretical massNumber of molelcules
Total (without water)28,5541
Polymers28,5541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulose synthase subunit C


Theoretical massNumber of molelcules
Total (without water)28,5541
Polymers28,5541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cellulose synthase subunit C


Theoretical massNumber of molelcules
Total (without water)28,5541
Polymers28,5541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cellulose synthase subunit C


Theoretical massNumber of molelcules
Total (without water)28,5541
Polymers28,5541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cellulose synthase subunit C


Theoretical massNumber of molelcules
Total (without water)28,5541
Polymers28,5541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.810, 55.620, 165.020
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cellulose synthase subunit C


Mass: 28554.031 Da / Num. of mol.: 5 / Fragment: UNP residues 24-272
Source method: isolated from a genetically manipulated source
Details: chainB: S230A, G231A, D232A, T233A, V234A, D235A, S236A, R238A, T239A, Q240A
Source: (gene. exp.) Enterobacter sp. CJF-002 (bacteria) / Gene: bcsC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K0J1W8

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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: 3.71 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MES, sodium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONSPring-8 BL44XU20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 3, 2014
RAYONIX MX300HE2CCDApr 12, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 3.28→50 Å / Num. obs: 32542 / % possible obs: 98.6 % / Redundancy: 3.7 % / Net I/σ(I): 10.7
Reflection shellResolution: 3.27→3.47 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.69 / Rsym value: 0.803 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.272→47.695 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.88
RfactorNum. reflection% reflection
Rfree0.2565 2218 6.82 %
Rwork0.2124 --
obs0.2154 32524 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.272→47.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8741 0 0 0 8741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018864
X-RAY DIFFRACTIONf_angle_d1.411996
X-RAY DIFFRACTIONf_dihedral_angle_d16.073339
X-RAY DIFFRACTIONf_chiral_restr0.0591340
X-RAY DIFFRACTIONf_plane_restr0.0091614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2715-3.34260.38051300.32691812X-RAY DIFFRACTION98
3.3426-3.42040.33121410.30441870X-RAY DIFFRACTION99
3.4204-3.50590.31231360.27121907X-RAY DIFFRACTION98
3.5059-3.60060.28951320.2641833X-RAY DIFFRACTION99
3.6006-3.70660.35921420.24531920X-RAY DIFFRACTION99
3.7066-3.82620.27161340.23951846X-RAY DIFFRACTION99
3.8262-3.96280.29661360.23051905X-RAY DIFFRACTION99
3.9628-4.12140.26741350.21521871X-RAY DIFFRACTION99
4.1214-4.30890.2521390.2081907X-RAY DIFFRACTION99
4.3089-4.53590.21191380.18591863X-RAY DIFFRACTION99
4.5359-4.81980.24741440.17871898X-RAY DIFFRACTION99
4.8198-5.19150.23131370.18771922X-RAY DIFFRACTION99
5.1915-5.71320.25021440.21421917X-RAY DIFFRACTION99
5.7132-6.53810.25021400.20621916X-RAY DIFFRACTION99
6.5381-8.23050.2161440.18661939X-RAY DIFFRACTION99
8.2305-47.69960.2171460.18211980X-RAY DIFFRACTION97

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