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- PDB-6l7r: Crystal structure of Chaetomium GCP3 N-terminus and Mozart1 -

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Basic information

Entry
Database: PDB / ID: 6l7r
TitleCrystal structure of Chaetomium GCP3 N-terminus and Mozart1
Components
  • Mozart1
  • Putative spindle pole body component alp6 protein
KeywordsTRANSLATION / gamma tubulin complex / microprotien / microtubule
Function / homology
Function and homology information


microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / mitotic spindle pole body / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / microtubule nucleation / spindle pole body / gamma-tubulin binding / mitotic spindle assembly ...microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / mitotic spindle pole body / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / microtubule nucleation / spindle pole body / gamma-tubulin binding / mitotic spindle assembly / spindle / spindle pole / microtubule / cytoplasm
Similarity search - Function
Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal
Similarity search - Domain/homology
Mitotic-spindle organizing protein 1 / Putative spindle pole body component alp6 protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84813131157 Å
AuthorsHuang, T.L. / Wang, H.J. / Hsia, K.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Cell Rep / Year: 2020
Title: Promiscuous Binding of Microprotein Mozart1 to gamma-Tubulin Complex Mediates Specific Subcellular Targeting to Control Microtubule Array Formation.
Authors: Huang, T.L. / Wang, H.J. / Chang, Y.C. / Wang, S.W. / Hsia, K.C.
History
DepositionNov 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Putative spindle pole body component alp6 protein
B: Mozart1


Theoretical massNumber of molelcules
Total (without water)21,3142
Polymers21,3142
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-48 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.515, 61.989, 52.244
Angle α, β, γ (deg.)90.000, 119.205, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

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Components

#1: Protein Putative spindle pole body component alp6 protein / GCP3


Mass: 11821.466 Da / Num. of mol.: 1 / Fragment: N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063320 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SED1
#2: Protein Mozart1


Mass: 9492.858 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0002490 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZC6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris hydrochloride pH 8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9784 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.84→20 Å / Num. obs: 101437 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 29.5273447895 Å2 / CC1/2: 0.995 / Net I/σ(I): 26.1
Reflection shellResolution: 1.84→1.92 Å / Num. unique obs: 1621 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84813131157→19.9518531996 Å / SU ML: 0.193769979505 / Cross valid method: FREE R-VALUE / σ(F): 1.40459111588 / Phase error: 24.0380271756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225817314747 3232 9.99628850674 %
Rwork0.18805688641 29100 -
obs0.191834798649 32332 99.1718299491 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.1126660995 Å2
Refinement stepCycle: LAST / Resolution: 1.84813131157→19.9518531996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 0 97 1517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005524950160081439
X-RAY DIFFRACTIONf_angle_d0.7929049003591955
X-RAY DIFFRACTIONf_chiral_restr0.0437190048533234
X-RAY DIFFRACTIONf_plane_restr0.0056060696866258
X-RAY DIFFRACTIONf_dihedral_angle_d11.7966019429897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87570.3008921614481260.234374006661133X-RAY DIFFRACTION86.2919808088
1.8757-1.9050.2712087771981360.2285184648471215X-RAY DIFFRACTION100
1.905-1.93620.2735708954021470.2126618247841340X-RAY DIFFRACTION99.9327956989
1.9362-1.96950.2451923503371350.2086981819811201X-RAY DIFFRACTION100
1.9695-2.00530.2706290706091490.2177993075651330X-RAY DIFFRACTION100
2.0053-2.04390.2870754470961380.2016611429811238X-RAY DIFFRACTION100
2.0439-2.08550.2306731469151430.1995386113361279X-RAY DIFFRACTION100
2.0855-2.13080.2530887721671400.1907394512421298X-RAY DIFFRACTION100
2.1308-2.18030.2224604494811430.1895276088551270X-RAY DIFFRACTION100
2.1803-2.23480.2121592840041380.1923330634411275X-RAY DIFFRACTION100
2.2348-2.29510.23513225491390.1733984099551262X-RAY DIFFRACTION99.9286733238
2.2951-2.36260.2252326381711440.1864756731971283X-RAY DIFFRACTION100
2.3626-2.43870.2477605439761460.2012609852721290X-RAY DIFFRACTION99.9304105776
2.4387-2.52570.2452963577881380.1992087548041265X-RAY DIFFRACTION100
2.5257-2.62660.2108177047051400.1947354180471266X-RAY DIFFRACTION99.9289267946
2.6266-2.74590.2195293276811430.1961944535191287X-RAY DIFFRACTION100
2.7459-2.89020.2151335039671440.2086910625561284X-RAY DIFFRACTION100
2.8902-3.07070.2471698191571410.2060228369921262X-RAY DIFFRACTION100
3.0707-3.30680.1992509412651430.1991298X-RAY DIFFRACTION100
3.3068-3.63780.2164146515381420.1949219760791236X-RAY DIFFRACTION99.9274836838
3.6378-4.160.1969725714761430.1621487568611281X-RAY DIFFRACTION99.9298245614
4.16-5.22560.2016413370811400.1562724086481290X-RAY DIFFRACTION99.7906489881
5.2256-100.2656199534461340.1724538154641217X-RAY DIFFRACTION95.6798866856
Refinement TLS params.Method: refined / Origin x: -19.1395126694 Å / Origin y: 8.83757201141 Å / Origin z: 9.59516055196 Å
111213212223313233
T0.207859256778 Å20.00327340202777 Å20.00846390163678 Å2-0.183554144747 Å20.0435973714383 Å2--0.19691073341 Å2
L2.08588869001 °2-1.35270822037 °2-0.779925613016 °2-2.204625572 °21.03034970824 °2--1.34700440599 °2
S0.130512860449 Å °0.27013007781 Å °0.109795250091 Å °-0.18838715285 Å °-0.146908574822 Å °-0.145689047904 Å °-0.143218081317 Å °-0.1058100671 Å °0.0270594771246 Å °
Refinement TLS groupSelection details: all

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