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- PDB-3a8e: The structure of AxCesD octamer complexed with cellopentaose -

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Basic information

Entry
Database: PDB / ID: 3a8e
TitleThe structure of AxCesD octamer complexed with cellopentaose
ComponentsCellulose synthase operon protein D
KeywordsBIOSYNTHETIC PROTEIN / COMPLEX / OCTAMER / TETRAMER OF DIMERS / MOLECULE RING / CELLULOSE BIOSYNTHESIS / BCSD / TC
Function / homology
Function and homology information


cellulose biosynthetic process / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3790 / Alpha-Beta Plaits - #2590 / Cellulose synthase operon protein D, bacterial / Cellulose synthase subunit D superfamily / Cellulose synthase subunit D / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta-cellopentaose / Cellulose synthase operon protein D
Similarity search - Component
Biological speciesAcetobacter xylinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsHu, S.Q. / Tajima, K. / Zhou, Y. / Yao, M. / Tanaka, I.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of bacterial cellulose synthase subunit D octamer with four inner passageways
Authors: Hu, S.Q. / Gao, Y.G. / Tajima, K. / Sunagawa, N. / Zhou, Y. / Kawano, S. / Fujiwara, T. / Yoda, T. / Shimura, D. / Satoh, Y. / Munekata, M. / Tanaka, I. / Yao, M.
#1: Journal: Protein Pept.Lett. / Year: 2008
Title: Purification, crystallization and preliminary X-ray studies of AxCesD required for efficient cellulose biosynthesis in Acetobacter xylinum
Authors: Yao, M. / Hu, S.Q. / Gao, Y.G. / Tajima, K. / Yoda, T. / Shimura, D. / Satoh, Y. / Kawano, S. / Tanaka, I. / Munekata, M.
History
DepositionOct 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose synthase operon protein D
B: Cellulose synthase operon protein D
C: Cellulose synthase operon protein D
D: Cellulose synthase operon protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3577
Polymers72,8714
Non-polymers2,4863
Water3,207178
1
A: Cellulose synthase operon protein D
B: Cellulose synthase operon protein D
C: Cellulose synthase operon protein D
D: Cellulose synthase operon protein D
hetero molecules

A: Cellulose synthase operon protein D
B: Cellulose synthase operon protein D
C: Cellulose synthase operon protein D
D: Cellulose synthase operon protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,71414
Polymers145,7428
Non-polymers4,9726
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area22170 Å2
ΔGint-137 kcal/mol
Surface area53510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.877, 132.877, 216.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11D-203-

HOH

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Components

#1: Protein
Cellulose synthase operon protein D / Cellulose synthase subunit D / AxCesD


Mass: 18217.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter xylinus (bacteria) / Strain: ATCC 23769 / Gene: acsD / Plasmid: PET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P37719
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.28 Å3/Da / Density % sol: 62.51 % / Mosaicity: 0.392 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M PHOSPHATE-CITRATE, 0.2M LI2SO4, 10% (V/V) ISO-PROPANOL, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19771 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 70.456 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Χ2: 1.017 / Net I/σ(I): 24.067
Reflection shellResolution: 3→3.11 Å / Redundancy: 9 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.41 / Num. unique all: 1944 / Rsym value: 0.399 / Χ2: 0.697 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
LAFIREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z9F

2z9f
PDB Unreleased entry


Resolution: 3→19.94 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 35.882 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; LAFIRE was also used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.29259 1925 9.8 %RANDOM
Rwork0.24178 ---
obs0.24677 19682 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.634 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 3→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 0 168 178 5174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.0147071
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.73624.105229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.52515827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.861538
X-RAY DIFFRACTIONr_chiral_restr0.0940.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2770.22763
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.23460
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.2163
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4981.53112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88524928
X-RAY DIFFRACTIONr_scbond_it0.49132298
X-RAY DIFFRACTIONr_scangle_it0.8724.52143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.002→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 147 -
Rwork0.309 1254 -
obs--100 %
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)
10.06030.00431.39620.00030.098732.3170.26270.1848-0.68530.25140.3016-0.67231.51531.9767-0.56430.3433-0.0968-0.05440.4321-0.07990.384662.27484.200198.6902
25.411-2.20841.08754.1238-0.81092.4864-0.2066-0.55590.55460.52450.108-0.2799-0.57180.30060.0986-0.0604-0.1081-0.044-0.0038-0.1057-0.194268.608716.4985122.1649
32.99390.57941.17551.38110.3975.4246-0.0008-0.28760.22120.098-0.08460.4237-0.0477-0.72060.0854-0.25360.01480.08470.0249-0.0428-0.065640.67937.1399108.9796
41.99130.07790.13882.84151.63345.7101-0.10940.12670.5006-0.07190.09730.0553-0.83920.05050.0121-0.0903-0.0421-0.0918-0.22320.0923-0.02659.184825.703788.5536
54.1969-2.3081-0.96084.9261.64372.7436-0.07880.5852-0.3172-0.3485-0.15350.48940.1227-0.57820.2323-0.2005-0.1919-0.06290.09-0.0287-0.126750.0476-2.272475.0951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 10
2X-RAY DIFFRACTION1B4 - 10
3X-RAY DIFFRACTION1C4 - 10
4X-RAY DIFFRACTION1D4 - 10
5X-RAY DIFFRACTION2A11 - 150
6X-RAY DIFFRACTION3B11 - 150
7X-RAY DIFFRACTION4C11 - 150
8X-RAY DIFFRACTION5D11 - 150

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