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- PDB-4g3a: Crystal Structure of MAST/Orbit N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4g3a
TitleCrystal Structure of MAST/Orbit N-terminal domain
ComponentsCLIP-associating protein
KeywordsCELL CYCLE / TOG domain / HEAT repeat / MAP protein / microtubule
Function / homology
Function and homology information


ovarian fusome organization / germline ring canal / spindle envelope / cystoblast division / spectrosome / hemocyte migration / fusome / oocyte microtubule cytoskeleton organization / contractile ring / basal cortex ...ovarian fusome organization / germline ring canal / spindle envelope / cystoblast division / spectrosome / hemocyte migration / fusome / oocyte microtubule cytoskeleton organization / contractile ring / basal cortex / mitotic spindle elongation / establishment of mitotic spindle localization / polar microtubule / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / regulation of mitotic centrosome separation / microtubule associated complex / microtubule organizing center / spindle organization / oogenesis / stem cell population maintenance / mitotic sister chromatid segregation / cleavage furrow / chromosome, centromeric region / mitotic spindle assembly / regulation of microtubule polymerization or depolymerization / spindle assembly / cytoplasmic microtubule / positive regulation of microtubule polymerization / mitotic spindle organization / axon guidance / spindle microtubule / mitotic spindle / kinetochore / microtubule cytoskeleton organization / spindle / spindle pole / mitotic cell cycle / growth cone / microtubule binding / nuclear membrane / centrosome / GTP binding / nucleus / cytoplasm
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe ...CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
CLIP-associating protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.994 Å
AuthorsDe la Mora-Rey, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The structure of the TOG-like domain of Drosophila melanogaster Mast/Orbit.
Authors: De la Mora-Rey, T. / Guenther, B.D. / Finzel, B.C.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLIP-associating protein
B: CLIP-associating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1354
Polymers54,9512
Non-polymers1842
Water3,801211
1
A: CLIP-associating protein


Theoretical massNumber of molelcules
Total (without water)27,4761
Polymers27,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CLIP-associating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6603
Polymers27,4761
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.180, 97.579, 149.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CLIP-associating protein / Misexpression suppressor of ras 7 / Protein Multiple asters / Mast / Protein Orbit / Protein chromosome bows


Mass: 27475.510 Da / Num. of mol.: 2 / Fragment: UNP residues 1-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG32435, chb, CLASP, Mast, MESR7, orbit / Plasmid: pET-29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NBD7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12.5% PEG 4000, 0.1M Bis-Tris, 0.1M NaCl & 20% v/v glycerol with a 1:1 ratio of protein to precipitant, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.994→82 Å / Num. all: 37109 / Num. obs: 36131 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 28.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.994→48.789 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1810 5.01 %Random
Rwork0.1876 ---
obs0.1897 36113 97.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.592 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.8005 Å20 Å2-0 Å2
2---0.4403 Å20 Å2
3----10.3602 Å2
Refinement stepCycle: LAST / Resolution: 1.994→48.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 12 211 3899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073774
X-RAY DIFFRACTIONf_angle_d1.0145106
X-RAY DIFFRACTIONf_dihedral_angle_d16.8171439
X-RAY DIFFRACTIONf_chiral_restr0.068590
X-RAY DIFFRACTIONf_plane_restr0.005659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.994-2.06520.2831500.21162774X-RAY DIFFRACTION81
2.0652-2.14790.25641760.1973311X-RAY DIFFRACTION95
2.1479-2.24560.22822010.18593421X-RAY DIFFRACTION99
2.2456-2.3640.25781790.18143433X-RAY DIFFRACTION99
2.364-2.51210.25051650.18943484X-RAY DIFFRACTION99
2.5121-2.70610.23681680.20643514X-RAY DIFFRACTION100
2.7061-2.97840.24911870.20283524X-RAY DIFFRACTION100
2.9784-3.40920.25872070.1963478X-RAY DIFFRACTION100
3.4092-4.29490.17551890.15973594X-RAY DIFFRACTION100
4.2949-48.80410.20921880.17583770X-RAY DIFFRACTION100
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)
10.229-0.1047-0.35140.73850.44231.01930.484-0.14550.1557-0.3276-0.8157-0.0448-0.20410.82050.39240.5686-0.01510.12550.92610.18690.39853.426633.68976.9762
20.412-0.6269-1.07031.32371.81162.85050.22690.10470.3717-0.04330.1698-0.3472-0.30930.3485-0.08440.63420.33580.31252.14280.94620.958514.229532.055711.9509
31.50090.2239-0.24782.7239-2.52515.91-0.00730.41650.0235-0.2601-0.0642-0.1588-0.00160.06210.08220.2346-0.02160.06510.29450.05240.2445-1.347729.572123.6244
42.0832-1.1244-0.66771.074-0.63962.966-0.0266-0.30150.1687-0.0610.1044-0.0914-0.01170.1156-0.07140.21190.02040.00310.2032-0.00970.2527-1.017721.833344.103
51.2996-0.7812-0.55880.5726-0.02891.14860.0259-0.47950.0243-0.04390.0452-0.06130.15310.1263-0.05490.36330.1112-0.00480.3310.03170.2049-4.387522.73558.1049
63.3128-0.6461-0.69960.3234-0.49761.7803-0.03920.1699-0.1442-0.0984-0.2159-0.180.25450.0570.20990.20510.05180.06160.22310.01540.283819.418352.037830.5772
70.04140.41690.30430.9112-1.79543.0265-0.0346-0.00150.07420.00310.05310.06360.0244-0.1101-0.02060.20940.06650.01910.2563-0.00410.290813.917348.030647.4122
81.06970.0236-0.21180.7794-1.57323.14550.0794-0.1565-0.0270.0635-0.16050.0145-0.17230.10040.05190.2920.01070.00030.2825-0.00920.256716.014142.034465.9536
90.7239-0.0384-0.77332.5493-1.69271.8709-0.0071-0.18410.02520.8472-0.1080.1536-0.72330.09650.09870.4657-0.1313-0.02780.38920.02350.217717.283941.116479.3446
101.9856-0.6563-0.25120.25930.18480.3169-0.13740.88970.2317-0.15510.1509-0.31130.3755-0.26240.10820.6686-0.4654-0.17620.84570.09480.47930.753949.313280.4067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:20)
2X-RAY DIFFRACTION2(chain A and resid 21:25)
3X-RAY DIFFRACTION3(chain A and resid 26:136)
4X-RAY DIFFRACTION4(chain A and resid 137:192)
5X-RAY DIFFRACTION5(chain A and resid 193:231)
6X-RAY DIFFRACTION6(chain B and resid 4:40)
7X-RAY DIFFRACTION7(chain B and resid 41:140)
8X-RAY DIFFRACTION8(chain B and resid 141:192)
9X-RAY DIFFRACTION9(chain B and resid 193:225)
10X-RAY DIFFRACTION10(chain B and resid 226:235)

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