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- PDB-6tj0: Crystal structure of the bacterial cellulose secretion regulator ... -

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Basic information

Entry
Database: PDB / ID: 6tj0
TitleCrystal structure of the bacterial cellulose secretion regulator BcsE, residues 217-523, with bound c-di-GMP.
ComponentsBacterial cellulose synthesis subunit E
KeywordsSIGNALING PROTEIN / Bacterial biofilms / Bacterial cellulose / Bacterial secretion system / c-di-GMP binding protein / GIL domain
Function / homologyCellulose biosynthesis protein BcsE / Cellulose biosynthesis protein BcsE / cellulose biosynthetic process / cyclic-di-GMP binding / Chem-C2E / Cyclic di-GMP binding protein BcsE
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZouhir, S. / Abidi, W. / Krasteva, P.V.
Funding support5items
OrganizationGrant numberCountry
European Research Council
Institute for Integrative Biology of the Cell (I2BC)
European Institute of Chemistry and Biology (IECB)
Centre National de la Recherche Scientifique (CNRS)
ATIP-Avenir starting grant
CitationJournal: Mbio / Year: 2020
Title: Structure and Multitasking of the c-di-GMP-Sensing Cellulose Secretion Regulator BcsE.
Authors: Zouhir, S. / Abidi, W. / Caleechurn, M. / Krasteva, P.V.
History
DepositionNov 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
Item: _audit_author.name / _citation.year ..._audit_author.name / _citation.year / _citation_author.name / _struct.title
Revision 1.2Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial cellulose synthesis subunit E
B: Bacterial cellulose synthesis subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4465
Polymers70,5722
Non-polymers8753
Water2,702150
1
A: Bacterial cellulose synthesis subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3782
Polymers35,2861
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacterial cellulose synthesis subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0683
Polymers35,2861
Non-polymers7832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.510, 112.510, 106.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Bacterial cellulose synthesis subunit E / Cellulose biosynthesis protein BcsE


Mass: 35285.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PURIFIED,UNTAGGED BCSE217-523 SELENOMETHIONINE-DERIVATIZED PROTEIN CRYSTALLIZED IN THE PRESENCE OF C-DI-GMP
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bcsE, yhjS, b3536, JW3504 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37657
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M 2-(N-morpholino)ethanesulfonic acid pH6, 0.2M Magnesium chloride, 4% PEG 4000, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911, 0.97927
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.979271
ReflectionResolution: 2.2→50 Å / Num. obs: 66468 / % possible obs: 99.4 % / Redundancy: 9.13 % / Biso Wilson estimate: 50.37 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.052 / Rrim(I) all: 0.217 / Net I/σ(I): 9.11
Reflection shellResolution: 2.2→2.33 Å / Mean I/σ(I) obs: 0.81 / Num. unique obs: 10635 / CC1/2: 0.458 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PHENIXAUTOBUILDmodel building
BUCCANEERmodel building
PHASERv2.5.7phasing
HKL2MapVersion 2016phasing
XDSVERSION Nov 1, 2016data processing
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.73 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1759 5.01 %RANDOM
Rwork0.205 ---
obs0.207 35118 99.6 %-
Displacement parametersBiso mean: 59.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.616 Å20 Å20 Å2
2--2.616 Å20 Å2
3----5.2321 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.2→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 58 150 4299
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094272HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055840HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1517SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes639HARMONIC5
X-RAY DIFFRACTIONt_it4272HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion16.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion560SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4866SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2496 141 5.02 %
Rwork0.2528 2669 -
all0.2526 2810 -
obs--99.33 %
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)
10.30510.7311-0.24642.8716-0.63590.4127-0.0311-0.0215-0.04830.13170.0345-0.04010.03490.0302-0.0034-0.22740.0296-0.0231-0.26460.00810.358844.7542134.278126.83
20.3312-0.7890.23323.9674-0.69540.23160.01550.11220.025-0.0034-0.0394-0.20780.02180.06160.0238-0.2969-0.0089-0.0014-0.2985-0.0030.387642.470987.7611111.135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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