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- PDB-4qmh: The XMAP215 family drives microtubule polymerization using a stru... -

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Basic information

Entry
Database: PDB / ID: 4qmh
TitleThe XMAP215 family drives microtubule polymerization using a structurally diverse TOG array
ComponentsLP04448p
KeywordsPROTEIN BINDING / TOG DOMAIN
Function / homology
Function and homology information


establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation ...establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation / microtubule plus-end binding / endoplasmic reticulum organization / oogenesis / microtubule polymerization / establishment of mitotic spindle orientation / centrosome duplication / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / axon guidance / spindle / kinetochore / spindle pole / mitotic cell cycle / microtubule binding / centrosome / cytoplasm
Similarity search - Function
XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant ...XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / 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
Protein mini spindles
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.652 Å
AuthorsFox, J.C. / Howard, A.E. / Currie, J.D. / Rogers, S.L. / Slep, K.C.
CitationJournal: Mol.Biol.Cell / Year: 2014
Title: The XMAP215 family drives microtubule polymerization using a structurally diverse TOG array.
Authors: Fox, J.C. / Howard, A.E. / Currie, J.D. / Rogers, S.L. / Slep, K.C.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: LP04448p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4002
Polymers26,3041
Non-polymers961
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.788, 32.613, 59.795
Angle α, β, γ (deg.)100.05, 95.23, 109.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LP04448p / Mini spindles / isoform C


Mass: 26303.529 Da / Num. of mol.: 1 / Fragment: TOG domain 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG5000, CG5000 Dmel_CG5000, Dmel_CG5000, msps / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 De3 Plyss / References: UniProt: Q9VEZ3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15 mg/ml protein concentration, 21% PEG 4000, 100 mM Tris pH 8.5, and 400 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12714, 0.97957
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 8, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.127141
20.979571
ReflectionResolution: 1.65→70 Å / Num. all: 45402 / Num. obs: 25054 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.021 / Net I/σ(I): 33
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 2355 / Rsym value: 0.117 / % possible all: 88.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.652→29.907 Å / SU ML: 0.18 / σ(F): 0.05 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1971 7.98 %Random 10%
Rwork0.1568 ---
all0.1593 24711 --
obs0.1593 24711 93.85 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.103 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6406 Å20.6933 Å2-1.0468 Å2
2--1.6385 Å2-0.1227 Å2
3----0.9978 Å2
Refinement stepCycle: LAST / Resolution: 1.652→29.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 5 401 2211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061843
X-RAY DIFFRACTIONf_angle_d1.0032491
X-RAY DIFFRACTIONf_dihedral_angle_d10.046694
X-RAY DIFFRACTIONf_chiral_restr0.061281
X-RAY DIFFRACTIONf_plane_restr0.005323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6516-1.69290.30151180.20971420X-RAY DIFFRACTION81
1.6929-1.73870.22671460.19641507X-RAY DIFFRACTION88
1.7387-1.78990.251260.19321564X-RAY DIFFRACTION90
1.7899-1.84760.19811370.16651629X-RAY DIFFRACTION93
1.8476-1.91360.17991450.15221595X-RAY DIFFRACTION93
1.9136-1.99030.1811450.1541622X-RAY DIFFRACTION94
1.9903-2.08080.21391420.15751644X-RAY DIFFRACTION95
2.0808-2.19050.22971460.15421649X-RAY DIFFRACTION96
2.1905-2.32770.18331410.15961680X-RAY DIFFRACTION96
2.3277-2.50730.19031470.14671680X-RAY DIFFRACTION97
2.5073-2.75950.17711380.15781650X-RAY DIFFRACTION97
2.7595-3.15840.1911500.15831695X-RAY DIFFRACTION98
3.1584-3.97780.16041470.13761704X-RAY DIFFRACTION98
3.9778-29.91190.15371430.15741701X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 24.1554 Å / Origin y: 10.4333 Å / Origin z: 10.0088 Å
111213212223313233
T0.045 Å2-0.0065 Å20.0014 Å2-0.0405 Å20.004 Å2--0.0464 Å2
L0.4646 °2-0.1672 °2-0.168 °2-0.4397 °20.1493 °2--0.3843 °2
S-0.0065 Å °-0.0356 Å °-0.0096 Å °-0.0081 Å °0.0205 Å °0.0239 Å °0.0112 Å °0.0435 Å °-0.0028 Å °
Refinement TLS groupSelection details: all

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