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- PDB-6tzk: Bacterial cellulose synthase outermembrane channel BcsC with term... -

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Basic information

Entry
Database: PDB / ID: 6tzk
TitleBacterial cellulose synthase outermembrane channel BcsC with terminal TPR repeat
ComponentsCellulose synthase operon protein C
KeywordsMEMBRANE PROTEIN / Porin / polysaccharide secretion / cellulose synthase
Function / homology
Function and homology information


cellulose biosynthetic process / outer membrane
Similarity search - Function
Cellulose synthase operon C, C-terminal / Cellulose synthase operon protein C C-terminus (BCSC_C) / : / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / HEXANE-1,6-DIOL / Cellulose synthase operon protein C
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.852 Å
AuthorsAcheson, J.F. / Derewenda, Z. / Zimmer, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM101001 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM126647-01 United States
CitationJournal: Structure / Year: 2019
Title: Architecture of the Cellulose Synthase Outer Membrane Channel and Its Association with the Periplasmic TPR Domain.
Authors: Acheson, J.F. / Derewenda, Z.S. / Zimmer, J.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Feb 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose synthase operon protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5117
Polymers50,3891
Non-polymers2,1226
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.713, 73.721, 85.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1332-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cellulose synthase operon protein C


Mass: 50389.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: bcsC, yhjL, b3530, JW5942 / Plasmid: pet20b_10Xhis_TEV_BcsC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P37650
#2: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 424 molecules

#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: Thin rectangular plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris 8.5, 200 mM CaCl2 and 30 - 40% PEG 400, 3% 1,6-hexanediol
PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 47945 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Χ2: 0.937 / Net I/σ(I): 11.5 / Num. measured all: 329823
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.885.60.51123870.8990.2320.5630.89799.8
1.88-1.926.30.47723350.9270.2040.5190.899100
1.92-1.956.60.41323640.9430.1720.4490.92399.7
1.95-1.996.90.33523690.9670.1370.3630.946100
1.99-2.047.20.28923730.9720.1150.3110.91599.8
2.04-2.087.20.25923620.9780.1030.2790.91299.9
2.08-2.147.10.23823720.9790.0950.2570.926100
2.14-2.1970.19923760.9840.080.2150.90199.8
2.19-2.266.80.18223650.9810.0750.1970.93899.9
2.26-2.336.10.15223660.9820.0660.1660.88499.7
2.33-2.416.90.14623710.9840.0590.1580.89399.8
2.41-2.517.50.1324100.9830.0510.1390.90299.8
2.51-2.627.50.11723760.9880.0460.1260.888100
2.62-2.767.30.10423940.9890.0410.1110.92599.9
2.76-2.947.10.09824220.990.0390.1050.96100
2.94-3.166.90.0924050.9890.0370.0980.9599.9
3.16-3.486.10.08324060.9880.0360.0910.93899.3
3.48-3.987.60.08424410.9920.0320.091.018100
3.98-5.017.30.08224650.9920.0320.0881.02100
5.01-306.60.08825860.9870.0360.0951.07399.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.852→28.312 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.13
RfactorNum. reflection% reflection
Rfree0.1831 2004 4.2 %
Rwork0.1641 --
obs0.1649 47684 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.75 Å2 / Biso mean: 27.7986 Å2 / Biso min: 6.95 Å2
Refinement stepCycle: final / Resolution: 1.852→28.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 143 419 4116
Biso mean--50.68 37.62 -
Num. residues----451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.852-1.89830.29071380.2316309195
1.8983-1.94970.20991400.1931320599
1.9497-2.0070.2041420.16233204100
2.007-2.07180.17391370.15863229100
2.0718-2.14580.20531430.16123269100
2.1458-2.23170.21391410.15813234100
2.2317-2.33320.20561450.15683229100
2.3332-2.45620.18491450.15813291100
2.4562-2.60990.18261440.15693253100
2.6099-2.81130.19041440.15523265100
2.8113-3.09390.18841420.16133294100
3.0939-3.54080.15661480.1536329699
3.5408-4.45830.13571430.14923351100
4.4583-28.3120.19581520.19346999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.37270.3029-2.08341.02661.63457.13540.2263-0.43890.14270.39740.16810.0989-0.55420.3355-0.32210.2953-0.01170.04120.29160.00110.157126.724419.407676.1024
23.7830.1935-0.47984.43250.5563.23060.0226-0.57380.13820.44720.10170.54560.2556-0.63250.03360.18280.00650.04180.26890.03890.208920.426712.084369.785
31.2483-0.17210.9640.5603-0.45521.37070.07770.1910.0219-0.1037-0.0447-0.05370.1420.0808-0.03440.12060.01250.04090.10150.00910.136121.81515.437432.3286
41.4165-0.08420.86611.7541.21293.29440.06510.20.2214-0.0385-0.1304-0.1276-0.0895-0.11880.01690.09840.01180.01550.08260.04810.149116.196822.787429.2652
53.26340.7282-3.79982.5636-4.31899.4529-0.2906-0.9377-0.2021.21370.24840.35860.7796-0.4312-0.00490.5925-0.15340.21381.2856-0.1126-0.11880.336624.240256.4207
61.592-0.19480.04950.9767-0.71260.89260.0234-0.27940.07650.16130.07080.0348-0.1536-0.1099-0.07790.1232-0.014-0.00630.13840.01420.11323.68117.711440.2795
71.3791-0.08140.26980.57590.1816-0.08120.05560.2290.0492-0.16330.02470.06320.0205-0.0983-0.040.13490.009-0.00290.14810.00950.11435.02215.986724.0329
81.168-0.33281.57361.0588-0.70153.48110.0639-0.0561-0.0961-0.08360.08920.0230.145-0.2347-0.15530.10560.0001-0.00210.07890.01690.156118.96456.455847.7434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 707:750)A707 - 750
2X-RAY DIFFRACTION2(chain A and resid 751:783)A751 - 783
3X-RAY DIFFRACTION3(chain A and resid 784:905)A784 - 905
4X-RAY DIFFRACTION4(chain A and resid 906:950)A906 - 950
5X-RAY DIFFRACTION5(chain A and resid 951:955)A951 - 955
6X-RAY DIFFRACTION6(chain A and resid 956:1043)A956 - 1043
7X-RAY DIFFRACTION7(chain A and resid 1044:1098)A1044 - 1098
8X-RAY DIFFRACTION8(chain A and resid 1099:1157)A1099 - 1157

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