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- PDB-3mxz: Crystal Structure of tubulin folding cofactor A from Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 3mxz
TitleCrystal Structure of tubulin folding cofactor A from Arabidopsis thaliana
ComponentsTubulin-specific chaperone A
KeywordsCHAPERONE / helix bundle
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / beta-tubulin binding / tubulin binding / peroxisome / microtubule cytoskeleton / protein folding / cytosol
Similarity search - Function
Tubulin binding cofactor A / Tubulin binding cofactor A superfamily / Tubulin binding cofactor A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Tubulin-folding cofactor A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsLu, L. / Nan, J. / Mi, W. / Su, X.D. / Li, Y.
Citation
Journal: Febs Lett. / Year: 2010
Title: Crystal structure of tubulin folding cofactor A from Arabidopsis thaliana and its beta-tubulin binding characterization
Authors: Lu, L. / Nan, J. / Mi, W. / Li, L.F. / Wei, C.H. / Su, X.D. / Li, Y.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thaliana
Authors: Lu, L. / Nan, J. / Mi, W. / Wei, C.H. / Li, L.F. / Li, Y.
History
DepositionMay 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin-specific chaperone A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2533
Polymers13,1291
Non-polymers1242
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.974, 54.974, 67.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-506-

NO3

21A-506-

NO3

31A-128-

HOH

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Components

#1: Protein Tubulin-specific chaperone A


Mass: 13128.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KIS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O04350
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.94 Å3/Da / Density % sol: 36.59 % / Mosaicity: 0.245 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 35% PEG3350, 0.4M Sodium Nitrate, 0.1M Sodium Acetate, pH 4.6, vapor diffusion, sitting drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8015 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 1.599→20 Å / Num. obs: 13258 / % possible obs: 99.8 % / Biso Wilson estimate: 16 Å2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.24 / Num. unique all: 1305 / Χ2: 0.787 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSD
Resolution: 1.599→17.683 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.862 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 653 4.93 %
Rwork0.176 --
obs0.177 13246 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.513 Å2 / ksol: 0.403 e/Å3
Displacement parametersBiso max: 102.71 Å2 / Biso mean: 23.147 Å2 / Biso min: 2.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.554 Å2-0 Å20 Å2
2---0.554 Å2-0 Å2
3---1.026 Å2
Refinement stepCycle: LAST / Resolution: 1.599→17.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 8 188 1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007832
X-RAY DIFFRACTIONf_angle_d1.0641096
X-RAY DIFFRACTIONf_chiral_restr0.059128
X-RAY DIFFRACTIONf_plane_restr0.004143
X-RAY DIFFRACTIONf_dihedral_angle_d12.663319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.599-1.7230.2771280.2082509263799
1.723-1.8960.2311250.19225272652100
1.896-2.170.221360.15624842620100
2.17-2.7320.1731360.16125162652100
2.732-17.6840.2041280.17525572685100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9697-0.66410.07993.66961.53012.1910.104-0.08540.0809-0.0320.0772-0.4093-1.0115-0.3818-0.07690.2692-0.0172-0.07720.1886-0.02290.191743.033938.613118.3262
21.28060.85770.76260.63930.9651.13540.0898-0.1490.14570.3973-0.02560.09640.21360.0116-0.0677-0.036-0.0283-0.03940.0548-0.00560.020230.785822.657918.0346
32.06670.50471.0761.0096-0.48242.04130.2322-0.1293-0.280.06390.05520.13540.08710.1148-0.10920.1202-0.0062-0.03870.10280.04060.122415.75382.874717.8599
4-0.0582-0.31520.9610.00940.38971.27020.0793-0.0461-0.42510.06570.13870.02190.1238-0.0739-0.18740.1146-0.0369-0.04110.11460.07160.20348.04512.816412.1159
50.71890.9011-1.03091.2257-0.4131.2963-0.18550.10080.2212-0.14470.23760.14390.07430.0851-0.0330.1638-0.0288-0.02520.12710.00620.104322.883315.60668.9058
62.92511.27132.93011.29751.342.3178-0.13210.7096-0.2196-0.22710.3225-0.0615-0.18710.5189-0.17350.105-0.05470.01320.2223-0.05140.087936.046325.36929.6822
7-2.5045-4.45983.8018-4.55430.15330.0707-0.26250.80860.3817-0.05120.0019-0.6775-0.20050.13450.24090.1639-0.12320.04860.3818-0.03030.355148.383833.039411.6706
82.21862.55230.06280.7032-0.0995-0.0195-0.09620.2609-0.21620.13640.1521-0.4349-0.0916-0.0214-0.07390.11520.0048-0.04720.1452-0.05440.228546.325127.33321.0879
90.5047-0.11660.8397-0.22771.271.99470.05210.2346-0.9117-0.1951-0.12280.0940.4194-0.0565-0.01160.17450.0104-0.0290.1945-0.0670.355338.84317.072714.8089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:6)A0 - 6
2X-RAY DIFFRACTION2(chain A and resid 7:26)A7 - 26
3X-RAY DIFFRACTION3(chain A and resid 27:40)A27 - 40
4X-RAY DIFFRACTION4(chain A and resid 41:56)A41 - 56
5X-RAY DIFFRACTION5(chain A and resid 57:67)A57 - 67
6X-RAY DIFFRACTION6(chain A and resid 68:78)A68 - 78
7X-RAY DIFFRACTION7(chain A and resid 79:87)A79 - 87
8X-RAY DIFFRACTION8(chain A and resid 88:100)A88 - 100
9X-RAY DIFFRACTION9(chain A and resid 101:107)A101 - 107

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