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- PDB-5ojh: Crystal structure of the extramembrane domain of the cellulose bi... -

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Basic information

Entry
Database: PDB / ID: 5ojh
TitleCrystal structure of the extramembrane domain of the cellulose biosynthetic protein BcsG from Salmonella typhimurium
ComponentsCellulose biosynthesis protein BcsG
KeywordsTRANSFERASE / Cellulose biosynthesis / biofilm / metalloenzyme / alkaline phosphatase family
Function / homologyCellulose biosynthesis protein BcsG / Cellulose biosynthesis protein BcsG / cellulose biosynthetic process / plasma membrane / CITRATE ANION / Cellulose biosynthesis protein BcsG
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchneider, G. / Vella, P. / Lindqvist, Y. / Schnell, R.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium.
Authors: Sun, L. / Vella, P. / Schnell, R. / Polyakova, A. / Bourenkov, G. / Li, F. / Cimdins, A. / Schneider, T.R. / Lindqvist, Y. / Galperin, M.Y. / Schneider, G. / Romling, U.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 biosynthesis protein BcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5744
Polymers42,1301
Non-polymers4443
Water5,639313
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-4 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.444, 80.444, 97.529
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-603-

FLC

21A-603-

FLC

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Components

#1: Protein Cellulose biosynthesis protein BcsG


Mass: 42130.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Gene: bcsG, STM3624 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q7CPI7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.55→69.7 Å / Num. obs: 53454 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 14 Å2 / Rpim(I) all: 0.056 / Rsym value: 0.116 / Net I/σ(I): 15.3
Reflection shellResolution: 1.55→1.59 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2609 / Rpim(I) all: 0.26 / Rsym value: 0.79 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ab initio model from Rosetta

Resolution: 1.55→69.67 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.387 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19831 2714 5.1 %RANDOM
Rwork0.16584 ---
obs0.16746 50696 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.55→69.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 27 313 3279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193229
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9634437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42524.805154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78315528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.671516
X-RAY DIFFRACTIONr_chiral_restr0.1060.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0391.2041577
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6721.7971980
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6081.3531649
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.30116.9375081
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 177 -
Rwork0.23 3691 -
obs--99.92 %

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