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- PDB-3feh: Crystal structure of full length centaurin alpha-1 -

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Basic information

Entry
Database: PDB / ID: 3feh
TitleCrystal structure of full length centaurin alpha-1
ComponentsCentaurin-alpha-1
KeywordsHydrolase activator / Structural Genomics Consortium / GAP / GTPase activation / SGC / Metal-binding / Nucleus / Phosphoprotein / Zinc-finger / METAL BINDING PROTEIN
Function / homology
Function and homology information


inositol 1,3,4,5 tetrakisphosphate binding / phosphatidylinositol bisphosphate binding / regulation of GTPase activity / phosphatidylinositol-3,4,5-trisphosphate binding / Nuclear signaling by ERBB4 / GTPase activator activity / cell surface receptor signaling pathway / intracellular membrane-bounded organelle / nucleus / metal ion binding ...inositol 1,3,4,5 tetrakisphosphate binding / phosphatidylinositol bisphosphate binding / regulation of GTPase activity / phosphatidylinositol-3,4,5-trisphosphate binding / Nuclear signaling by ERBB4 / GTPase activator activity / cell surface receptor signaling pathway / intracellular membrane-bounded organelle / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ADAP, PH domain 1 / ADAP, PH domain 2 / Arf GTPase activating protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Annexin V; domain 1 ...ADAP, PH domain 1 / ADAP, PH domain 2 / Arf GTPase activating protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Annexin V; domain 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Arf-GAP with dual PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsShen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Phosphorylation-independent dual-site binding of the FHA domain of KIF13 mediates phosphoinositide transport via centaurin {alpha}1.
Authors: Tong, Y. / Tempel, W. / Wang, H. / Yamada, K. / Shen, L. / Senisterra, G.A. / Mackenzie, F. / Chishti, A.H. / Park, H.W.
History
DepositionNov 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Dec 27, 2023Group: 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: Centaurin-alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0654
Polymers45,0001
Non-polymers653
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.055, 52.380, 65.023
Angle α, β, γ (deg.)90.000, 106.450, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe authors state that the biological unit is unknown.

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Components

#1: Protein Centaurin-alpha-1 / Putative MAPK-activating protein PM25


Mass: 44999.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENTA1 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O75689
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.342.586456
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, sitting drop6.525% PEG3350, 0.2M ammonium sulfate, 0.1M Bis-Tris, pH 6.5, vapor diffusion, sitting drop, temperature 291K
2912vapor diffusion, hanging drop630% PEG3350, 0.2M ammonium sulfate, 0.1M Bis-Tris, pH 6, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.96863
SYNCHROTRONAPS 19-ID20.97923, 0.97940
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 5, 2007
MARMOSAIC 300 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.968631
20.979231
30.97941
Reflection

Av σ(I) over netI: 7.2 / D res high: 2.5 Å / D res low: 25 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2Num. obs% possible obs
6.91980050.1511.6714184100
6.82957930.1691.661409399.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.372510010.0593.3546.5
4.275.3710010.0641.9896.6
3.734.2710010.0891.9286.9
3.393.7310010.1231.6577
3.153.3910010.2051.4067
2.963.1510010.3231.3147.1
2.822.9610010.4621.3587.1
2.692.8210010.6451.2627.1
2.592.6910010.7771.2337
2.52.5999.910.991.176.7
5.372510020.0643.5336.5
4.275.3710020.0691.9646.6
3.734.2710020.0991.8216.9
3.393.7310020.1411.5767
3.153.3910020.2371.3477.1
2.963.1510020.3731.2617.1
2.822.9610020.5441.2587.1
2.692.8210020.7181.2357
2.592.6999.620.841.2486.6
2.52.5997.220.961.2156
ReflectionResolution: 1.9→50 Å / Num. obs: 27553 / % possible obs: 91.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.083 / Χ2: 1.894
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.971.70.37716071.60753.8
1.97-2.0520.31322331.08474.7
2.05-2.142.50.28627331.37390.8
2.14-2.252.90.2329261.27397.4
2.25-2.393.30.19730151.20499.3
2.39-2.583.60.15329981.36599.8
2.58-2.843.70.11729941.64399.8
2.84-3.253.60.08730282.00999.7
3.25-4.093.50.06230332.71799.5
4.09-503.30.05629863.52695.8

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.61 Å / D res low: 25 Å / FOM : 0.33 / Reflection: 11666
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se50.4290.6590.1630.0831.011
2Se600.5440.1710.4711.118
3Se17.6480.2680.3550.2480.728
4Se600.2060.2960.4090.746
5Se600.1020.2280.4730.745
Phasing MAD shell
Resolution (Å)FOM Reflection
9.07-250.64659
5.83-9.070.611057
4.59-5.830.541291
3.91-4.590.421503
3.46-3.910.341668
3.13-3.460.231768
2.89-3.130.151850
2.69-2.890.11870

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.11phasing
RESOLVEphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.9→37.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.205 / SU B: 4.309 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1374 4.99 %RANDOM
Rwork0.209 ---
obs0.211 27536 91.106 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.925 Å2
2--0.223 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 3 136 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222944
X-RAY DIFFRACTIONr_bond_other_d0.0020.022040
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.933994
X-RAY DIFFRACTIONr_angle_other_deg1.80234895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20922.781151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4351525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213354
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02683
X-RAY DIFFRACTIONr_mcbond_it1.66921786
X-RAY DIFFRACTIONr_mcbond_other0.4712718
X-RAY DIFFRACTIONr_mcangle_it2.57232851
X-RAY DIFFRACTIONr_scbond_it1.88221158
X-RAY DIFFRACTIONr_scangle_it2.91431141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9490.42530.2641067220050.909
1.949-2.0030.235630.2461380215666.929
2.003-2.0610.283750.231604209780.067
2.061-2.1240.261810.2231774204190.887
2.124-2.1930.2571080.2171825199996.698
2.193-2.270.256980.221769190498.057
2.27-2.3550.316760.2181738183099.126
2.355-2.4510.284920.2181704180199.722
2.451-2.560.212840.2041615170499.707
2.56-2.6840.276930.2061557165399.819
2.684-2.8290.264790.2131469155499.614
2.829-2.9990.253810.2271386147499.525
2.999-3.2050.266640.2281333140099.786
3.205-3.460.273730.2091215129299.69
3.46-3.7880.219590.1941145121399.258
3.788-4.230.199630.1781006107499.534
4.23-4.8750.222440.16790096797.622
4.875-5.9490.315420.20777483098.313
5.949-8.3230.241360.24159664897.531
8.323-40.1930.291100.22130538781.395

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