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- PDB-6pd0: Crystal structure of the bacterial cellulose synthase subunit G (... -

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Basic information

Entry
Database: PDB / ID: 6pd0
TitleCrystal structure of the bacterial cellulose synthase subunit G (BcsG) from Escherichia coli, catalytic domain
ComponentsCellulose biosynthesis protein BcsG
KeywordsTRANSFERASE / Cellulose / Biofilm / Phosphoethanolamine
Function / homologyCellulose biosynthesis protein BcsG / Cellulose biosynthesis protein BcsG / cellulose biosynthetic process / plasma membrane / Cellulose biosynthesis protein BcsG
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAnderson, A.C. / Brenner, T. / Weadge, J.T.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)630044 Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: TheEscherichia colicellulose synthase subunit G (BcsG) is a Zn2+-dependent phosphoethanolamine transferase.
Authors: Anderson, A.C. / Burnett, A.J.N. / Hiscock, L. / Maly, K.E. / Weadge, J.T.
History
DepositionJun 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
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 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose biosynthesis protein BcsG
B: Cellulose biosynthesis protein BcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9005
Polymers90,7862
Non-polymers1143
Water17,601977
1
A: Cellulose biosynthesis protein BcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4823
Polymers45,3931
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulose biosynthesis protein BcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4172
Polymers45,3931
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.510, 76.920, 95.920
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellulose biosynthesis protein BcsG


Mass: 45392.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bcsG, yhjU, b3538, JW3506 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37659
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 977 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES:NaOH, 20% (w/v) PEG 4000, 10% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationMonochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→47.96 Å / Num. obs: 74391 / % possible obs: 96.64 % / Redundancy: 7 % / Biso Wilson estimate: 18.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0435 / Rpim(I) all: 0.01794 / Rrim(I) all: 0.04711 / Net I/σ(I): 28.56
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.2657 / Mean I/σ(I) obs: 7.42 / Num. unique obs: 6595 / CC1/2: 0.969 / Rpim(I) all: 0.1126 / Rrim(I) all: 0.2894 / % possible all: 85.96

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PCZ

6pcz


Resolution: 1.75→47.958 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 3720 5 %
Rwork0.1608 --
obs0.1627 74374 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→47.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 3 977 6686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075860
X-RAY DIFFRACTIONf_angle_d1.0217976
X-RAY DIFFRACTIONf_dihedral_angle_d3.3813488
X-RAY DIFFRACTIONf_chiral_restr0.056864
X-RAY DIFFRACTIONf_plane_restr0.0061052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.77220.25721070.25372023X-RAY DIFFRACTION77
1.7722-1.79550.24631260.20962398X-RAY DIFFRACTION88
1.7955-1.82010.24111360.18932582X-RAY DIFFRACTION96
1.8201-1.84610.23381350.17842559X-RAY DIFFRACTION96
1.8461-1.87370.21561390.18162635X-RAY DIFFRACTION96
1.8737-1.9030.24221340.19682558X-RAY DIFFRACTION96
1.903-1.93420.21481390.19142637X-RAY DIFFRACTION96
1.9342-1.96750.28461370.18452593X-RAY DIFFRACTION96
1.9675-2.00330.211370.18452605X-RAY DIFFRACTION97
2.0033-2.04180.24071370.17472612X-RAY DIFFRACTION97
2.0418-2.08350.23241390.17332633X-RAY DIFFRACTION97
2.0835-2.12880.27441370.17412604X-RAY DIFFRACTION97
2.1288-2.17830.23581390.17172640X-RAY DIFFRACTION97
2.1783-2.23280.23511380.16922627X-RAY DIFFRACTION98
2.2328-2.29320.22271400.16232651X-RAY DIFFRACTION98
2.2932-2.36060.20271380.16492626X-RAY DIFFRACTION98
2.3606-2.43680.20261390.16082644X-RAY DIFFRACTION98
2.4368-2.52390.20841410.16042674X-RAY DIFFRACTION98
2.5239-2.6250.21381410.15752688X-RAY DIFFRACTION98
2.625-2.74440.18891410.1612671X-RAY DIFFRACTION99
2.7444-2.88910.20151400.16032659X-RAY DIFFRACTION99
2.8891-3.07010.18531410.15892691X-RAY DIFFRACTION99
3.0701-3.30710.18871420.15572700X-RAY DIFFRACTION99
3.3071-3.63980.17161420.14582686X-RAY DIFFRACTION99
3.6398-4.16620.15521430.13782727X-RAY DIFFRACTION100
4.1662-5.2480.14671450.13322747X-RAY DIFFRACTION100
5.248-47.97560.191470.1612784X-RAY DIFFRACTION100

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