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- PDB-3aj2: The structure of AxCeSD octamer (C-terminal HIS-tag) from Acetoba... -

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Basic information

Entry
Database: PDB / ID: 3aj2
TitleThe structure of AxCeSD octamer (C-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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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: 2Z9F
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)72,8714
Polymers72,8714
Non-polymers00
Water4,702261
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

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


Theoretical massNumber of molelcules
Total (without water)145,7428
Polymers145,7428
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area21300 Å2
ΔGint-134 kcal/mol
Surface area53820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.351, 133.351, 217.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
Cellulose synthase operon protein D


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 / Plasmid: PET-28 / 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.: 261 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.4
Details: 0.2M LI2SO4, 0.1M PHOSPHATE-CITRATE pH 5.4, 10% (V/V) ISO-PROPANOL, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 27157 / Num. obs: 27157 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 20.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.432 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z9E

2z9e
PDB Unreleased entry


Resolution: 2.7→19.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 22.737 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27551 2691 9.9 %RANDOM
Rwork0.2089 ---
obs0.21553 24434 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: 64.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 0 261 5046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9626648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0035603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.73923.973224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.35915821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1321539
X-RAY DIFFRACTIONr_chiral_restr0.1280.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023694
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2740.22610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23280
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2331
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9081.53095
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61724891
X-RAY DIFFRACTIONr_scbond_it2.05232030
X-RAY DIFFRACTIONr_scangle_it3.4624.51757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 210 -
Rwork0.35 1681 -
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)
12.2401-1.7511-0.5594.6690.58541.9273-0.03520.5436-0.2536-0.2488-0.10320.40740.2151-0.4540.1384-0.1842-0.1777-0.05620.0505-0.0054-0.102650.6475-1.957175.6423
21.65490.05190.18971.56451.04254.7352-0.05610.17270.4507-0.01060.0631-0.0506-0.7009-0.0181-0.007-0.0708-0.0986-0.0744-0.19540.0942-0.030159.456525.566288.8117
33.9649-1.9270.01062.4127-0.2971.5269-0.1949-0.47330.36070.51090.1496-0.2016-0.39350.2450.0453-0.0047-0.0976-0.0453-0.0871-0.0819-0.150568.578916.0435122.4168
42.27140.39381.29381.18990.52134.7395-0.0053-0.19550.00220.14650.00380.32820.0123-0.75370.0015-0.2095-0.03320.0896-0.06-0.0177-0.110341.1227.1612109.3437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 150
2X-RAY DIFFRACTION2B10 - 150
3X-RAY DIFFRACTION3C10 - 150
4X-RAY DIFFRACTION4D10 - 150

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