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- PDB-3d8b: Crystal structure of human fidgetin-like protein 1 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3d8b
TitleCrystal structure of human fidgetin-like protein 1 in complex with ADP
ComponentsFidgetin-like protein 1
KeywordsHYDROLASE / AAA+ / ATPase / ADP / SGC / Structural Genomics Consortium / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


microtubule severing ATPase activity / osteoblast proliferation / male meiotic nuclear division / Resolution of D-loop Structures through Holliday Junction Intermediates / regulation of double-strand break repair via homologous recombination / nuclear chromosome / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / cellular response to ionizing radiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...microtubule severing ATPase activity / osteoblast proliferation / male meiotic nuclear division / Resolution of D-loop Structures through Holliday Junction Intermediates / regulation of double-strand break repair via homologous recombination / nuclear chromosome / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / cellular response to ionizing radiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Meiotic recombination / osteoblast differentiation / hydrolase activity / regulation of cell cycle / negative regulation of apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Vps4 oligomerisation, C-terminal / : / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 ...: / Vps4 oligomerisation, C-terminal / : / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Fidgetin-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKarlberg, T. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Karlberg, T. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Welin, M. / Wikstrom, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human fidgetin-like protein 1.
Authors: Karlberg, T. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / ...Authors: Karlberg, T. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Welin, M. / Wikstrom, M. / Schuler, H.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Fidgetin-like protein 1
B: Fidgetin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8684
Polymers79,0142
Non-polymers8542
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-10.1 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.430, 85.430, 197.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-174-

HOH

DetailsAUTHORS STATE THAT THE DIMER THAT IS PRESENT IN THE ASYMMETRIC UNIT IS POSSIBLY THE BIOLOGICAL ASSEMBLY

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Components

#1: Protein Fidgetin-like protein 1


Mass: 39506.980 Da / Num. of mol.: 2 / Fragment: AAA+ ATPase domain: Residues 341-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIGNL1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE
References: UniProt: Q6PIW4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M NaCl, 0.1M Bis-Tris, 0.02M ADP, 0.01M MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 49968 / Num. obs: 49968 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 20
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 5.2 / Num. unique all: 6683 / Rsym value: 0.556 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B9P

3b9p


Resolution: 2→24.99 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.573 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23669 2499 5 %RANDOM
Rwork0.19713 ---
all0.19909 47466 --
obs0.19909 47466 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 54 283 4651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224456
X-RAY DIFFRACTIONr_bond_other_d0.0020.023119
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9986035
X-RAY DIFFRACTIONr_angle_other_deg0.94337621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88624.108185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18815800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5811535
X-RAY DIFFRACTIONr_chiral_restr0.0850.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
X-RAY DIFFRACTIONr_nbd_refined0.2110.2916
X-RAY DIFFRACTIONr_nbd_other0.1970.23202
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22214
X-RAY DIFFRACTIONr_nbtor_other0.0840.22288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9511.52890
X-RAY DIFFRACTIONr_mcbond_other0.1911.51110
X-RAY DIFFRACTIONr_mcangle_it1.49224502
X-RAY DIFFRACTIONr_scbond_it2.17131804
X-RAY DIFFRACTIONr_scangle_it3.5244.51530
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 181 -
Rwork0.194 3440 -
obs--100 %
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)
10.57550.0085-0.00070.67380.05690.26200.00560.0854-0.0434-0.0114-0.02930.0701-0.04280.0114-0.0183-0.0367-0.0156-0.01680.008-0.0146-54.54-4.1830.207
20.8999-0.31930.11611.1304-0.40860.4533-0.060.00410.0806-0.00250.04620.1236-0.007-0.13980.0138-0.0335-0.0132-0.0202-0.0092-0.00070.0098-65.0852.0153.585
31.90310.44760.91740.2630.42930.97190.05780.0054-0.02720.0658-0.0040.01010.20810.0562-0.05380.0087-0.0077-0.0181-0.02630.008-0.0465-43.244-11.46720.459
40.73140.45630.0250.7564-0.15120.55210.0195-0.05530.02430.0249-0.05050.03160.00870.07860.031-0.0346-0.03260.00020.00450.0028-0.03-34.0398.65310.591
51.66390.577-0.473.1272-0.7781.48020.0911-0.08930.34540.1407-0.08020.4235-0.07090.0597-0.0108-0.0709-0.0420.0197-0.0456-0.02390.0797-41.30220.99111.132
60.28810.43930.36121.26820.83630.7911-0.0250.0306-0.0121-0.06920.0649-0.01980.01410.1445-0.0399-0.0168-0.02310.0102-0.00450.0064-0.0419-33.23-0.726-7.68
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA374 - 47457 - 157
2X-RAY DIFFRACTION2AA475 - 556158 - 239
3X-RAY DIFFRACTION3AA557 - 674240 - 357
4X-RAY DIFFRACTION4BB379 - 47162 - 154
5X-RAY DIFFRACTION5BB477 - 537160 - 220
6X-RAY DIFFRACTION6BB538 - 672221 - 355

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