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- PDB-3aj1: The structure of AxCeSD octamer (N-terminal HIS-tag) from Acetoba... -

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Basic information

Entry
Database: PDB / ID: 3aj1
TitleThe structure of AxCeSD octamer (N-terminal HIS-tag) from Acetobacter xylinum
ComponentsCellulose synthase operon protein D
KeywordsBIOSYNTHETIC PROTEIN / ALPHA AND BETA FOLD / OCTAMER / TETRAMER OF DIMERS / MOLECULE RING / CELLULOSE BIOSYNTHESIS / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES
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
Cellulose synthase operon protein D
Similarity search - Component
Biological speciesACETOBACTER XYLINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHu, S.Q. / Tajima, K. / Zhou, Y. / Tanaka, I. / Yao, M.
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
DepositionMay 20, 2010Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 6, 2010ID: 2Z9E
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
E: Cellulose synthase operon protein D
F: Cellulose synthase operon protein D
G: Cellulose synthase operon protein D
H: Cellulose synthase operon protein D


Theoretical massNumber of molelcules
Total (without water)151,9098
Polymers151,9098
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.700, 77.700, 213.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Cellulose synthase operon protein D


Mass: 18988.656 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACETOBACTER XYLINUS (bacteria) / Strain: ATCC 23769 / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P37719
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.1M LITHIUM SULFATE, 0.1M N-(2-ACETAMIDE) IMINODIACETIC ACID PH 6.5, 12%(W/V) POLYETHYLENE GLYCOL 4000, 2%(V/V) ISO-PROPANOL, EVAPORATION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9790, 0.9793, 0.9000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 14, 2006
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.91
ReflectionResolution: 2.45→50 Å / Num. all: 51353 / Num. obs: 51353 / % possible obs: 98.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 10.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.423 / % possible all: 86.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.326 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25708 4883 9.9 %RANDOM
Rwork0.20333 ---
obs0.2086 44637 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.319 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9539 0 0 392 9931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229718
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.97313235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58651214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.19724.163430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.098151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4041580
X-RAY DIFFRACTIONr_chiral_restr0.0960.21540
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217305
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_it0.8431.56064
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59229834
X-RAY DIFFRACTIONr_scbond_it2.03933654
X-RAY DIFFRACTIONr_scangle_it3.3364.53401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 329 -
Rwork0.254 3019 -
obs--93.83 %

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