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- PDB-6i5c: Long wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex -

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Basic information

Entry
Database: PDB / ID: 6i5c
TitleLong wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex
Components
  • Stathmin-4
  • TUBULIN-TYROSINE LIGASE
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsSTRUCTURAL PROTEIN / Tubulin complex / T2R-TTL / Long-wavelength native-SAD phasing / native-SAD / S-SAD
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family ...Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (cattle)
Rattus norvegicus (Norway rat)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsBasu, S. / Olieric, V. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Leonarski, F. / Yamada, Y. / Vera, L. / Olieric, N. ...Basu, S. / Olieric, V. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Leonarski, F. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Diederichs, K. / Yamamoto, M. / Bunk, O. / Wang, M.
Citation
Journal: Iucrj / Year: 2019
Title: Long-wavelength native-SAD phasing: opportunities and challenges.
Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Bunk, O. / Diederichs, K. ...Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Bunk, O. / Diederichs, K. / Yamamoto, M. / Wang, M.
#1: Journal: Iucrj / Year: 2019
Title: Long-wavelength native-SAD phasing: opportunities and challenges
Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Diederichs, K. / ...Authors: Basu, S. / Olieric, V. / Leonarski, F. / Matsugaki, N. / Kawano, Y. / Takashi, T. / Huang, C.Y. / Yamada, Y. / Vera, L. / Olieric, N. / Basquin, J. / Wojdyla, J.A. / Diederichs, K. / Yamamoto, M. / Bunk, O. / Wang, M.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMar 13, 2019ID: 4WBN
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Revision 2.0Aug 21, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq
Item: _atom_site.label_entity_id / _entity_name_com.entity_id ..._atom_site.label_entity_id / _entity_name_com.entity_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 2.1Sep 23, 2020Group: Database references / Derived calculations
Category: pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.2May 15, 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: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: TUBULIN-TYROSINE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,65823
Polymers254,4866
Non-polymers3,17317
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23090 Å2
ΔGint-175 kcal/mol
Surface area79210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.240, 156.830, 179.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and (resid 1 through 439 or resid 501 through 504))
12(chain B and (resid 2 through 276 or resid 286 through 438 or resid 505))
22(chain D and (resid 2 through 438 or resid 502))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 439
211(chain C and (resid 1 through 439 or resid 501 through 504))C1 - 439
221(chain C and (resid 1 through 439 or resid 501 through 504))C501 - 504
112(chain B and (resid 2 through 276 or resid 286 through 438 or resid 505))B2 - 276
122(chain B and (resid 2 through 276 or resid 286 through 438 or resid 505))B286 - 438
132(chain B and (resid 2 through 276 or resid 286 through 438 or resid 505))B505
212(chain D and (resid 2 through 438 or resid 502))D0

NCS ensembles :
ID
1
2

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48966.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 48391.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16082.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein TUBULIN-TYROSINE LIGASE


Mass: 43687.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 8 types, 481 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG, 16% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 11135360 / % possible obs: 99.9 % / Redundancy: 177.76 % / CC1/2: 1 / Net I/σ(I): 52.23
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 137.02 % / Mean I/σ(I) obs: 3.29 / Num. unique obs: 625357 / CC1/2: 0.823 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.95→49.46 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.17
RfactorNum. reflection% reflection
Rfree0.2082 5970 4.99 %
Rwork0.1699 --
obs0.1719 119616 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.24 Å2 / Biso mean: 73.5155 Å2 / Biso min: 29.58 Å2
Refinement stepCycle: final / Resolution: 2.95→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17247 0 185 464 17896
Biso mean--72.04 66.34 -
Num. residues----2178
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4108X-RAY DIFFRACTION8.587TORSIONAL
12C4108X-RAY DIFFRACTION8.587TORSIONAL
21B4010X-RAY DIFFRACTION8.587TORSIONAL
22D4010X-RAY DIFFRACTION8.587TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-2.98350.45231950.46713718391398
2.9835-3.01860.38612040.378838014005100
3.0186-3.05540.35061960.314338184014100
3.0554-3.09410.35131990.276337793978100
3.0941-3.13480.31342000.243338284028100
3.1348-3.17770.23911960.221337153911100
3.1777-3.22310.28742000.229938004000100
3.2231-3.27120.31572030.249738174020100
3.2712-3.32230.35091970.255637483945100
3.3223-3.37680.2872010.23938004001100
3.3768-3.4350.2611980.210938144012100
3.435-3.49750.23461970.189537733970100
3.4975-3.56470.23362030.1838374040100
3.5647-3.63740.21911990.168337583957100
3.6374-3.71650.1882030.166238104013100
3.7165-3.80290.21811950.161637553950100
3.8029-3.8980.19151930.150238074000100
3.898-4.00340.20272050.150338294034100
4.0034-4.12110.17281910.140737373928100
4.1211-4.2540.20512010.139537973998100
4.254-4.4060.15961950.131238074002100
4.406-4.58230.15322030.124838154018100
4.5823-4.79070.14121940.12837633957100
4.7907-5.0430.16792010.141637863987100
5.043-5.35860.20152040.152637863990100
5.3586-5.77180.19231980.165138174015100
5.7718-6.35160.2012010.17537793980100
6.3516-7.26820.18732040.162437793983100
7.2682-9.14760.17121960.13837823978100
9.1476-49.46710.21071980.175337913989100

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