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- PDB-5j2t: Tubulin-vinblastine complex -

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Basic information

Entry
Database: PDB / ID: 5j2t
TitleTubulin-vinblastine complex
Components
  • Stathmin-4
  • TUBULIN-TYROSINE LIGASE
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / CYTOSKELETON / TUBULIN FOLD / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Helix hairpin bin / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Helix hairpin bin / 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, A domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 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. / Dna Ligase; domain 1 / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-VLB / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsWaight, A.B. / Bargsten, K. / Doronina, S. / Steinmetz, M.O. / Sussman, D. / Prota, A.E.
CitationJournal: Plos One / Year: 2016
Title: Structural Basis of Microtubule Destabilization by Potent Auristatin Anti-Mitotics.
Authors: Waight, A.B. / Bargsten, K. / Doronina, S. / Steinmetz, M.O. / Sussman, D. / Prota, A.E.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: TUBULIN-TYROSINE LIGASE
B: Tubulin beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,68316
Polymers261,6316
Non-polymers3,05210
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22540 Å2
ΔGint-123 kcal/mol
Surface area79860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.250, 157.740, 182.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 6 molecules ACDBEF

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


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: brain / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: brain / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 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: 44378.496 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 , 7 types, 340 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.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-VLB / (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE / VINBLASTINE


Mass: 810.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H58N4O9
#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.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.9 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6% PEG, 12% 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
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.2 Å / Num. obs: 150857 / % possible obs: 97.8 % / Redundancy: 12.9 % / Rsym value: 0.158 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 0.71 / Rsym value: 3.461 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4I4T

4i4t


Resolution: 2.2→48.168 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88
RfactorNum. reflection% reflection
Rfree0.244 7494 4.97 %
Rwork0.1934 --
obs0.1959 150775 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17264 0 195 330 17789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818004
X-RAY DIFFRACTIONf_angle_d1.07424474
X-RAY DIFFRACTIONf_dihedral_angle_d16.2136688
X-RAY DIFFRACTIONf_chiral_restr0.0422686
X-RAY DIFFRACTIONf_plane_restr0.0053169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.4572070.40544228X-RAY DIFFRACTION87
2.225-2.25120.35412750.35044551X-RAY DIFFRACTION95
2.2512-2.27860.38632420.35194775X-RAY DIFFRACTION99
2.2786-2.30750.36212470.33024830X-RAY DIFFRACTION99
2.3075-2.33780.38162640.31044771X-RAY DIFFRACTION99
2.3378-2.36990.32532640.2944766X-RAY DIFFRACTION99
2.3699-2.40370.32612570.294782X-RAY DIFFRACTION99
2.4037-2.43960.33132600.28654800X-RAY DIFFRACTION99
2.4396-2.47770.32892390.27544803X-RAY DIFFRACTION99
2.4777-2.51830.32212400.26624801X-RAY DIFFRACTION99
2.5183-2.56180.30312250.25084860X-RAY DIFFRACTION99
2.5618-2.60830.29142580.23164785X-RAY DIFFRACTION99
2.6083-2.65850.26622540.23154801X-RAY DIFFRACTION99
2.6585-2.71280.32672470.23534857X-RAY DIFFRACTION99
2.7128-2.77170.29262340.23764867X-RAY DIFFRACTION99
2.7717-2.83620.30632540.2474618X-RAY DIFFRACTION96
2.8362-2.90710.32932160.234476X-RAY DIFFRACTION92
2.9071-2.98570.28132560.2174841X-RAY DIFFRACTION99
2.9857-3.07360.26012690.19894799X-RAY DIFFRACTION100
3.0736-3.17280.2432620.18944888X-RAY DIFFRACTION100
3.1728-3.28610.28422450.19664872X-RAY DIFFRACTION100
3.2861-3.41770.27022880.18954801X-RAY DIFFRACTION99
3.4177-3.57320.2172460.17624909X-RAY DIFFRACTION99
3.5732-3.76150.21772380.16864901X-RAY DIFFRACTION99
3.7615-3.9970.1962490.16194814X-RAY DIFFRACTION99
3.997-4.30550.24082340.19644516X-RAY DIFFRACTION92
4.3055-4.73840.18562510.13524901X-RAY DIFFRACTION99
4.7384-5.42330.19312530.14084936X-RAY DIFFRACTION99
5.4233-6.82960.22982650.17694815X-RAY DIFFRACTION97
6.8296-48.17940.18752550.16484917X-RAY DIFFRACTION94
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)
10.72950.1272-0.07251.74060.73971.5758-0.06750.1351-0.0402-0.41030.3084-0.2955-0.56420.4540.00060.551-0.16730.1330.5331-0.19370.466432.748788.128852.4884
20.3036-0.0031-0.17061.64650.50762.01770.211-0.02110.06810.16790.0118-0.0041-0.1370.1257-0.00020.3552-0.01150.06190.3832-0.1470.404919.92382.506266.3748
30.75310.02180.40711.28740.90931.19780.0064-0.13690.01290.4145-0.00880.21530.02770.09360.00010.59490.00220.09640.4653-0.10060.453819.474583.510173.9293
40.12220.37590.12430.85180.21440.2702-0.0411-0.0483-0.20750.44070.4434-0.51160.61380.96930.02280.46750.1957-0.09640.6871-0.23830.591532.718561.595460.8711
50.06070.1316-0.01040.15080.05110.0169-0.11310.0085-0.17220.02720.0616-0.02990.2438-0.2161-0.0010.5386-0.02920.04760.5529-0.12540.545323.32572.825662.7809
60.8023-0.64140.4120.5433-0.49880.81160.10110.23540.1476-0.42390.01580.0753-0.5951-0.0622-0.00010.6388-0.0150.03390.3555-0.03280.46616.939870.912319.4295
70.2119-0.2671-0.28610.28380.25580.83550.01140.1195-0.1334-0.49170.2164-0.2919-0.26690.429-0.00010.3938-0.13250.06070.4743-0.10840.392129.127956.587514.5982
80.7773-0.5509-0.83330.42080.47591.1115-0.0391-0.1054-0.0187-0.0960.1876-0.1274-0.09850.25190.00010.3163-0.02750.0180.4045-0.09860.396324.046953.592626.0306
90.2647-0.3132-0.19110.42050.38150.30040.1745-0.35940.0442-0.0925-0.24940.13420.1311-0.30790.00010.3157-0.0047-0.02840.4814-0.12830.47135.092752.150528.0742
100.3775-0.0725-0.02340.92091.48132.25150.0082-0.06870.1294-0.1925-0.11410.1114-0.4052-0.2518-0.00240.38380.0641-0.01720.4242-0.11810.50989.587662.892535.1681
110.5495-0.4394-0.02870.58280.7441.1822-0.0663-0.13930.04470.1026-0.15660.2643-0.008-0.59230.00010.37730.07080.0110.5273-0.13150.47786.521161.973444.8178
120.0249-0.06430.4520.03660.12440.6713-0.0929-0.18810.00190.27610.09250.11070.36420.0344-0.00050.39230.01050.03350.4178-0.0630.42114.603242.973434.0102
130.35680.06260.26870.76630.03510.1355-0.1604-0.0989-0.34890.36680.0647-0.2340.50690.39150.00030.38470.0658-0.06520.4165-0.01750.409424.707938.53330.9416
140.5921-0.4851-0.13761.55250.29431.4872-0.01070.20290.0177-0.23540.0894-0.0347-0.12570.169200.2931-0.0960.02750.324-0.02050.324819.568633.0357-12.0607
150.32390.0872-0.20250.87490.92991.4097-0.06140.02920.08160.0081-0.03740.07750.1062-0.21400.2817-0.05440.01430.3387-0.03540.36337.130726.02193.111
160.504-0.42730.21060.4766-0.24690.4562-0.36390.98140.1228-0.32390.36540.22850.1305-0.66280.01840.7649-0.160.04351.1027-0.12720.473516.57239.051-44.0096
171.09290.4635-1.19081.10530.21012.3349-0.34560.5814-0.1794-0.32470.1408-0.12460.3546-0.3079-0.10.6032-0.1870.10760.692-0.2570.432820.1231-2.5761-33.2814
180.44980.0339-0.18470.8931-0.22191.72-0.30090.4653-0.2611-0.03240.14710.12170.4101-0.49070.00970.6313-0.2160.10050.6075-0.16730.52998.4938-4.1582-20.8802
190.25-0.33650.24860.32-0.31520.2581-0.40770.1203-0.42890.4194-0.01630.16621.18360.0979-0.00340.9176-0.02570.21990.5868-0.24110.670629.9062-16.4541-23.6905
200.41030.13060.18810.20790.46220.47750.2283-0.1210.18250.1913-0.0016-0.5064-0.12570.786400.8567-0.0952-0.04720.7002-0.14330.542528.272192.387382.9339
210.1632-0.373-0.6542-0.14220.3043-0.0293-0.0737-0.07770.04340.56070.2284-0.15230.66340.3240.05370.54830.04530.03940.6861-0.27770.588442.381529.04595.8051
220.77190.0569-1.07560.4751-0.10711.0909-0.42770.3747-0.5650.03930.16470.02950.7092-0.31110.00030.7779-0.11160.11720.5481-0.10370.61816.0955.239969.9332
230.7990.11140.3350.74150.62620.44680.0841-0.2687-0.28560.3176-0.0282-0.31950.33140.74370.00010.84670.1401-0.03380.96130.18590.700415.615457.5549104.4257
241.35410.2786-0.95260.8270.27031.7946-0.28180.0002-0.35360.29830.18290.08680.43990.119-0.01540.81550.11190.16470.39520.08020.572-1.685254.393293.585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 180)
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 311)
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 401)
4X-RAY DIFFRACTION4chain 'A' and (resid 402 through 436)
5X-RAY DIFFRACTION5chain 'A' and (resid 437 through 450)
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 88)
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 127)
8X-RAY DIFFRACTION8chain 'B' and (resid 128 through 197)
9X-RAY DIFFRACTION9chain 'B' and (resid 198 through 223)
10X-RAY DIFFRACTION10chain 'B' and (resid 224 through 295)
11X-RAY DIFFRACTION11chain 'B' and (resid 296 through 373)
12X-RAY DIFFRACTION12chain 'B' and (resid 374 through 401)
13X-RAY DIFFRACTION13chain 'B' and (resid 402 through 438)
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 197)
15X-RAY DIFFRACTION15chain 'C' and (resid 198 through 440)
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 88)
17X-RAY DIFFRACTION17chain 'D' and (resid 89 through 295)
18X-RAY DIFFRACTION18chain 'D' and (resid 296 through 401)
19X-RAY DIFFRACTION19chain 'D' and (resid 402 through 441)
20X-RAY DIFFRACTION20chain 'E' and (resid 6 through 46)
21X-RAY DIFFRACTION21chain 'E' and (resid 47 through 144)
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 66)
23X-RAY DIFFRACTION23chain 'F' and (resid 67 through 198)
24X-RAY DIFFRACTION24chain 'F' and (resid 199 through 384)

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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