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- PDB-4i86: Crystal structure of PilZ domain of CeSA from cellulose synthesiz... -

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Basic information

Entry
Database: PDB / ID: 4i86
TitleCrystal structure of PilZ domain of CeSA from cellulose synthesizing bacterium
ComponentsCellulose synthase 1
KeywordsTRANSFERASE / beta-barrel fold / c-di-GMP Binding
Function / homology
Function and homology information


cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / UDP-alpha-D-glucose metabolic process / cyclic-di-GMP binding / plasma membrane
Similarity search - Function
Cellulose synthase, subunit A / : / Cellulose synthase, subunit B / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 ...Cellulose synthase, subunit A / : / Cellulose synthase, subunit B / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cellulose synthase 1
Similarity search - Component
Biological speciesGluconacetobacter xylinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsFujiwara, T. / Komoda, K. / Sakurai, N. / Tanaka, I. / Yao, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: The c-di-GMP recognition mechanism of the PilZ domain of bacterial cellulose synthase subunit A
Authors: Fujiwara, T. / Komoda, K. / Sakurai, N. / Tajima, K. / Tanaka, I. / Yao, M.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulose synthase 1
B: Cellulose synthase 1


Theoretical massNumber of molelcules
Total (without water)24,5902
Polymers24,5902
Non-polymers00
Water1,11762
1
A: Cellulose synthase 1


Theoretical massNumber of molelcules
Total (without water)12,2951
Polymers12,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulose synthase 1


Theoretical massNumber of molelcules
Total (without water)12,2951
Polymers12,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.360, 59.500, 78.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellulose synthase 1 / CELLLOSE SYNTHASE SUBUNIT A / Cellulose synthase catalytic domain [UDP-forming] / Cyclic di-GMP- ...CELLLOSE SYNTHASE SUBUNIT A / Cellulose synthase catalytic domain [UDP-forming] / Cyclic di-GMP-binding domain / Cellulose synthase 1 regulatory domain


Mass: 12295.118 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP residues 572-670
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconacetobacter xylinus (bacteria) / Gene: acsAB / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0CW87, cellulose synthase (UDP-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.86 Å3/Da / Density % sol: 33.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M phosphate-citrate, 30%(v/v) PEG300, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 5, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.098→45 Å / Num. obs: 11236 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 24.52
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1767 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(AutoMR: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
PHENIX(AutoMR: 1.7.1_743)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.098→35.153 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8042 / SU ML: 0.47 / σ(F): 2.01 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 537 4.78 %RANDOM
Rwork0.2144 ---
obs0.2167 11226 99.82 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.971 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 68.9 Å2 / Biso mean: 33.8746 Å2 / Biso min: 14.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.3776 Å20 Å2-0 Å2
2---2.5412 Å20 Å2
3---6.9187 Å2
Refinement stepCycle: LAST / Resolution: 2.098→35.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 0 62 1587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081555
X-RAY DIFFRACTIONf_angle_d1.1472116
X-RAY DIFFRACTIONf_chiral_restr0.076250
X-RAY DIFFRACTIONf_plane_restr0.005271
X-RAY DIFFRACTIONf_dihedral_angle_d15.519568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0983-2.30940.27571410.226626052746
2.3094-2.64340.28861250.216926482773
2.6434-3.33010.28481340.211426412775
3.3301-35.15840.23871370.212427952932

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