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

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Basic information

Entry
Database: PDB / ID: 5olt
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 / CITRIC ACID / Cellulose biosynthesis protein BcsG
Function and homology information
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsVella, P. / Polyakova, A. / Lindqvist, Y. / Schnell, R. / Bourenkov, G. / Schneider, T. / Schneider, G.
Funding support Sweden, Germany, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
BMBF Germany
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 28, 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 / 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 1.2Nov 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

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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)42,5804
Polymers42,1301
Non-polymers4503
Water5,801322
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-7 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.658, 80.658, 97.673
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-602-

CIT

21A-705-

HOH

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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 typhimurium LT2 (bacteria) / Gene: bcsG, STM3624 / Production host: Escherichia coli DH5[alpha] / 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: ammonium citrate, ZnCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 1.45→69.85 Å / Num. obs: 60090 / % possible obs: 96.1 % / Redundancy: 9 % / Biso Wilson estimate: 9.8 Å2 / Rpim(I) all: 0.023 / Rsym value: 0.068 / Net I/σ(I): 21.3
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5 / Num. unique obs: 8728 / Rpim(I) all: 0.206 / Rsym value: 0.538 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→69.85 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.814 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15715 3279 5.2 %RANDOM
Rwork0.12657 ---
obs0.12812 60090 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.032 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.45→69.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 27 322 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193358
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9634621
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44724.936156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08615541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2141515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212714
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_it1.6271.5141670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.042.2782132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3971.7891682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.09422.295272
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.67233352
X-RAY DIFFRACTIONr_sphericity_free17.7895186
X-RAY DIFFRACTIONr_sphericity_bonded8.66453381
LS refinement shellResolution: 1.447→1.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 164 -
Rwork0.18 2949 -
obs--64.46 %

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