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

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Basic information

Entry
Database: PDB / ID: 6pcz
TitleCrystal structure of the bacterial cellulose synthase subunit G (BcsG) catalytic domain from Escherichia coli, selenomethionine variant
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 / SAD / Resolution: 1.44 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 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)91,9725
Polymers91,8172
Non-polymers1553
Water12,647702
1
A: Cellulose biosynthesis protein BcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9983
Polymers45,9091
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)45,9742
Polymers45,9091
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.710, 94.580, 105.190
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 biosynthesis protein BcsG


Mass: 45908.617 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M 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: 0.97965 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationMonochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 1.44→45.97 Å / Num. obs: 142124 / % possible obs: 99.99 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06236 / Rpim(I) all: 0.02631 / Rrim(I) all: 0.06776 / Net I/σ(I): 19.13
Reflection shellResolution: 1.44→1.491 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.051 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 14051 / CC1/2: 0.667 / Rpim(I) all: 0.4404 / Rrim(I) all: 1.14 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→45.97 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2083 7108 5 %
Rwork0.1963 --
obs0.1969 142124 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5671 0 3 702 6376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075822
X-RAY DIFFRACTIONf_angle_d0.8797925
X-RAY DIFFRACTIONf_dihedral_angle_d3.4332109
X-RAY DIFFRACTIONf_chiral_restr0.087861
X-RAY DIFFRACTIONf_plane_restr0.0061045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4399-1.45630.31712360.29764477X-RAY DIFFRACTION100
1.4563-1.47340.28542320.28454415X-RAY DIFFRACTION100
1.4734-1.49140.32842350.27724456X-RAY DIFFRACTION100
1.4914-1.51030.27272350.2534466X-RAY DIFFRACTION100
1.5103-1.53020.22752350.2364456X-RAY DIFFRACTION100
1.5302-1.55110.24212340.22774447X-RAY DIFFRACTION100
1.5511-1.57330.24442360.22644494X-RAY DIFFRACTION100
1.5733-1.59680.26072330.22644430X-RAY DIFFRACTION100
1.5968-1.62170.25092360.21884478X-RAY DIFFRACTION100
1.6217-1.64830.22982350.21934456X-RAY DIFFRACTION100
1.6483-1.67670.23032340.21564454X-RAY DIFFRACTION100
1.6767-1.70720.25562370.21794499X-RAY DIFFRACTION100
1.7072-1.74010.24852340.21464456X-RAY DIFFRACTION100
1.7401-1.77560.23822360.20734478X-RAY DIFFRACTION100
1.7756-1.81420.22722360.21234489X-RAY DIFFRACTION100
1.8142-1.85640.22072360.21424477X-RAY DIFFRACTION100
1.8564-1.90280.2432350.20924471X-RAY DIFFRACTION100
1.9028-1.95430.20782370.20844495X-RAY DIFFRACTION100
1.9543-2.01180.23262360.20054482X-RAY DIFFRACTION100
2.0118-2.07670.23262360.20364498X-RAY DIFFRACTION100
2.0767-2.15090.18772370.19874499X-RAY DIFFRACTION100
2.1509-2.23710.20492370.19554507X-RAY DIFFRACTION100
2.2371-2.33890.18382370.19274494X-RAY DIFFRACTION100
2.3389-2.46220.20932380.19874531X-RAY DIFFRACTION100
2.4622-2.61640.20322390.20054535X-RAY DIFFRACTION100
2.6164-2.81840.22812380.19894526X-RAY DIFFRACTION100
2.8184-3.1020.22832390.20184543X-RAY DIFFRACTION100
3.102-3.55070.21162420.18894591X-RAY DIFFRACTION100
3.5507-4.4730.17442430.16494609X-RAY DIFFRACTION100
4.473-47.31550.16312540.17434822X-RAY DIFFRACTION100

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