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- PDB-5mw9: Complex between the Leucine Zipper (LZ) and Centrosomin-motif 2 (... -

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Basic information

Entry
Database: PDB / ID: 5mw9
TitleComplex between the Leucine Zipper (LZ) and Centrosomin-motif 2 (CM2) domains of Drosophila melanogaster Centrosomin (Cnn) - L535E mutant form
Components(CentrosominCDK5RAP2) x 2
KeywordsCELL CYCLE / Centrosome / Centriole / Coiled-coil / Mitosis
Function / homology
Function and homology information


photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium ...photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium / centrosome cycle / midgut development / pericentriolar material / centriole replication / centriole / mitotic spindle organization / ciliary basal body / meiotic cell cycle / central nervous system development / spindle pole / molecular adaptor activity / centrosome / Golgi apparatus
Similarity search - Function
Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeng, Z. / Johnson, S. / Raff, J.W. / Lea, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104575 United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Cell / Year: 2017
Title: Structural Basis for Mitotic Centrosome Assembly in Flies.
Authors: Feng, Z. / Caballe, A. / Wainman, A. / Johnson, S. / Haensele, A.F.M. / Cottee, M.A. / Conduit, P.T. / Lea, S.M. / Raff, J.W.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomin
B: Centrosomin
C: Centrosomin
E: Centrosomin
F: Centrosomin
D: Centrosomin
H: Centrosomin
G: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,19010
Polymers59,0598
Non-polymers1312
Water1,38777
1
A: Centrosomin
B: Centrosomin
C: Centrosomin
D: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5955
Polymers29,5304
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-104 kcal/mol
Surface area15060 Å2
MethodPISA
2
E: Centrosomin
F: Centrosomin
H: Centrosomin
G: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5955
Polymers29,5304
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-116 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)275.792, 43.000, 48.350
Angle α, β, γ (deg.)90.00, 96.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Centrosomin / CDK5RAP2 / Protein arrow


Mass: 8198.428 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Centrosomin CM2 domain residues 1082-1148 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pLip / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P54623
#2: Protein
Centrosomin / CDK5RAP2 / Protein arrow


Mass: 6566.411 Da / Num. of mol.: 4 / Mutation: L535E
Source method: isolated from a genetically manipulated source
Details: Centrosomin LZ domain residues 490-544, L535E mutant
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pETM44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): B834 / References: UniProt: P54623
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.42 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 18%(w/v) PEG2KMME, 0.2M sodium cacodylate pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.2→31.355 Å / Num. obs: 27935 / % possible obs: 96.4 % / Redundancy: 2.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.046 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2406 / CC1/2: 0.769 / Rpim(I) all: 0.531 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→31.352 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.85
RfactorNum. reflection% reflection
Rfree0.3016 1240 4.45 %
Rwork0.2575 --
obs0.2594 27865 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→31.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 2 77 3730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023682
X-RAY DIFFRACTIONf_angle_d0.3114916
X-RAY DIFFRACTIONf_dihedral_angle_d8.1372345
X-RAY DIFFRACTIONf_chiral_restr0.025573
X-RAY DIFFRACTIONf_plane_restr0.001634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.40351670.37382895X-RAY DIFFRACTION95
2.2881-2.39220.31091340.30762917X-RAY DIFFRACTION95
2.3922-2.51830.3811250.30182953X-RAY DIFFRACTION96
2.5183-2.6760.32311350.29612925X-RAY DIFFRACTION95
2.676-2.88250.30381330.27922883X-RAY DIFFRACTION95
2.8825-3.17230.36881310.28322964X-RAY DIFFRACTION96
3.1723-3.63070.29151230.26333039X-RAY DIFFRACTION97
3.6307-4.57210.28271490.22732966X-RAY DIFFRACTION96
4.5721-31.35510.2671430.233083X-RAY DIFFRACTION96
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)
16.376-0.2268-2.42162.60720.31194.87070.15961.1969-0.1706-0.2176-0.2538-0.34330.5458-0.11020.0070.49770.06930.05970.29410.05810.470478.195611.55212.3739
23.75380.0947-2.89430.8848-0.53964.56590.5194-0.17450.41020.3431-0.1166-0.0568-0.4064-0.4584-0.18890.6816-0.12420.09390.3942-0.07820.588151.386812.694739.0629
37.11623.4803-4.02964.1098-2.32746.27030.0725-2.1372-2.122.5339-0.7468-1.0281-0.93820.00290.24411.8008-0.4440.38550.9312-0.05890.86432.0343.964665.6986
44.25362.3966-2.58724.3215-1.62343.8361-0.2801-0.09520.5925-0.31870.05450.25030.02971.05130.14570.56880.06060.05930.64170.13760.7188.115711.458915.0442
55.95830.6241-3.51862.1564-0.58792.260.0052-0.319-0.633-0.0527-0.1958-0.29390.05930.1760.14550.5454-0.00020.05790.2378-0.02530.615370.57065.27823.7549
67.14371.1819-4.52631.4371-1.27073.2499-0.13070.5806-0.713-0.0344-0.20290.33410.2389-0.99140.08580.4752-0.14610.05960.6669-0.19370.648236.51913.951236.9211
70.3909-0.0886-1.3897-0.00750.28384.81240.0134-0.62590.2707-0.13660.33450.2569-0.1892-0.444-0.20241.5904-0.45660.37272.2753-0.03331.5228-2.0323.932673.439
88.1411-3.7772-0.57562.2343-0.40661.10490.8740.55590.82910.4664-0.39161.5644-1.5865-1.1344-0.02271.8485-0.56230.79211.7158-0.73061.818711.91491.335862.5031
95.23890.9525-2.74831.1259-0.11932.47680.19590.04210.11150.8686-0.35480.52790.3095-0.62290.24570.8699-0.2050.27010.7293-0.25120.819732.0610.743751.2153
100.4314-0.35340.2330.71630.15390.5241-0.2302-0.0699-0.813-1.92110.64730.3442-1.1326-0.2767-0.14131.6085-0.05230.36311.61-0.20221.64767.55665.899777.8861
112.7501-1.2431.64552.4997-0.66211.40060.9267-0.2437-0.41860.62710.84570.6170.0344-0.70741.6451.1908-0.26150.7681.4652-0.6590.776121.19278.220461.8398
128.481.028-3.92874.13140.47177.17491.14360.11110.9090.982-0.05751.2411-0.9205-0.6261-0.45010.784-0.040.2230.7635-0.0890.719432.259712.118244.2761
130.26870.35740.12630.67920.15410.0557-0.2275-0.2016-0.3591-1.1775-0.36630.7881-0.6294-0.56430.05761.3197-0.110.12343.2697-0.09481.2458-29.6644-16.96348.5939
146.8605-0.6179-2.53331.8579-0.31983.3280.85790.5412-0.23360.32280.049-0.0172-0.5112-0.1945-0.70510.6770.2246-0.06531.3016-0.06250.5747-2.0689-13.640439.5324
153.3882-0.73030.52865.18710.09754.80140.4914-0.01091.382-0.117-0.45730.8435-2.1134-0.62270.64520.93910.16550.15081.09980.2081.076630.6841-9.512520.8224
160.61890.9945-0.58683.29080.24741.4038-0.668-0.37880.16311.3408-0.32310.7527-0.25080.1270.14490.94840.56960.23872.19480.58821.8549-30.2052-7.051948.1574
175.8974-1.3529-0.39840.4811-1.11490.66690.0799-0.018-1.3236-0.54170.11920.4148-0.2414-1.2399-0.00450.49860.1879-0.15251.993-0.16550.91164.1426-19.724129.4654
186.90530.98931.21642.3978-1.54241.47390.2109-0.1993-0.46191.0656-0.82090.05711.35950.76790.40870.82990.1256-0.05721.2283-0.43321.287643.2756-30.857921.9264
196.3805-1.22120.79044.9563-0.17325.179-0.01540.6998-0.61410.0004-0.0048-1.30981.6660.3546-0.15810.85560.19510.09830.5644-0.18420.772977.0621-33.35681.1946
209.9481-4.9916-0.54473.62110.32430.70120.35890.2342-0.687-0.2419-0.1214-0.15880.3528-0.3754-0.28150.6334-0.0963-0.01130.5773-0.1080.759455.429-29.23819.4764
215.3709-1.4516-1.1641.43420.09361.5831-0.09661.13120.4609-0.3268-0.0118-0.167-0.7284-1.08310.08770.52150.06070.00021.1603-0.08470.488228.9162-19.24917.0253
221.4111-0.9243-3.23960.64672.0357.4123-0.37490.43270.6768-1.0278-0.5094-0.818-0.7127-0.07720.42011.3059-0.06570.09951.3039-0.01050.929682.3648-29.4353-10.1732
239.5966-2.2901-3.64692.86011.50626.26470.66590.43061.3605-0.4356-0.2573-0.0276-0.5166-0.5428-0.0120.5007-0.010.03740.3916-0.02320.605765.7509-22.58344.6249
246.3735-0.5654-1.84491.67320.86182.94980.34830.12110.0202-0.2716-0.0584-0.1665-0.4375-0.1808-0.15310.4532-0.0307-0.00660.7931-0.16880.606736.6085-19.297124.7174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1081:1100)
2X-RAY DIFFRACTION2(chain A and resid 1101:1133)
3X-RAY DIFFRACTION3(chain A and resid 1134:1146)
4X-RAY DIFFRACTION4(chain B and resid 1079:1091)
5X-RAY DIFFRACTION5(chain B and resid 1092:1108)
6X-RAY DIFFRACTION6(chain B and resid 1109:1140)
7X-RAY DIFFRACTION7(chain C and resid 499:513)
8X-RAY DIFFRACTION8(chain C and resid 514:522)
9X-RAY DIFFRACTION9(chain C and resid 523:544)
10X-RAY DIFFRACTION10(chain D and resid 503:516)
11X-RAY DIFFRACTION11(chain D and resid 517:531)
12X-RAY DIFFRACTION12(chain D and resid 532:544)
13X-RAY DIFFRACTION13(chain E and resid 1082:1092)
14X-RAY DIFFRACTION14(chain E and resid 1093:1122)
15X-RAY DIFFRACTION15(chain E and resid 1123:1142)
16X-RAY DIFFRACTION16(chain F and resid 1082:1090)
17X-RAY DIFFRACTION17(chain F and resid 1091:1138)
18X-RAY DIFFRACTION18(chain F and resid 1139:1145)
19X-RAY DIFFRACTION19(chain G and resid 492:504)
20X-RAY DIFFRACTION20(chain G and resid 505:523)
21X-RAY DIFFRACTION21(chain G and resid 524:543)
22X-RAY DIFFRACTION22(chain H and resid 488:495)
23X-RAY DIFFRACTION23(chain H and resid 496:517)
24X-RAY DIFFRACTION24(chain H and resid 518:544)

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