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- PDB-9bkr: Crystal structure of the Human TRIP12 WWE domain (isoform 2) in c... -

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Basic information

Entry
Database: PDB / ID: 9bkr
TitleCrystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ATP
ComponentsIsoform 2 of E3 ubiquitin-protein ligase TRIP12
KeywordsLIGASE / TRIP12 / Isoform 2 / WWE / SGC / TRANSPORT PROTEIN / Structural Genomics Consortium / PSI-Biology / Protein Structure Initiative
Function / homologyHECT-type E3 ubiquitin transferase / ADENOSINE-5'-TRIPHOSPHATE / Isoform 2 of E3 ubiquitin-protein ligase TRIP12
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKimani, S. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ATP
Authors: Kimani, S. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
SupersessionJul 31, 2024ID: 8TRE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of E3 ubiquitin-protein ligase TRIP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6163
Polymers9,0911
Non-polymers5252
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.351, 33.492, 66.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 2 of E3 ubiquitin-protein ligase TRIP12 / E3 ubiquitin-protein ligase for Arf / ULF / HECT-type E3 ubiquitin transferase TRIP12 / Thyroid ...E3 ubiquitin-protein ligase for Arf / ULF / HECT-type E3 ubiquitin transferase TRIP12 / Thyroid receptor-interacting protein 12 / TR-interacting protein 12 / TRIP-12


Mass: 9090.911 Da / Num. of mol.: 1 / Fragment: WWE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP12, KIAA0045, ULF / Production host: Escherichia coli (E. coli)
References: UniProt: Q14669-2, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % P3350, 0.2 M Mg Cl, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 13611 / % possible obs: 97.9 % / Redundancy: 12.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.039 / Rrim(I) all: 0.134 / Χ2: 1.632 / Net I/σ(I): 7.9 / Num. measured all: 166083
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.4-1.424.50.7245250.1260.4740.4070.8430.778.2
1.42-1.455.90.6376270.8580.9610.2660.6950.63388.7
1.45-1.488.50.5966320.9360.9830.2010.630.73796.9
1.48-1.5110.20.5386840.9650.9910.1680.5650.71899.6
1.51-1.5411.50.5276770.9650.9910.160.5510.758100
1.54-1.58130.5176730.9780.9940.1480.5390.76899.9
1.58-1.6213.90.5276900.9650.9910.1470.5470.78499.7
1.62-1.6614.90.5016750.9830.9960.1350.520.826100
1.66-1.7114.80.4416770.980.9950.1210.4580.8899.9
1.71-1.7614.20.3776830.9680.9920.1070.3921.01399.3
1.76-1.8313.90.3136760.9510.9870.0890.3261.1499.1
1.83-1.915.20.2627060.980.9950.0740.2721.335100
1.9-1.9914.90.2396780.9790.9950.0690.2491.601100
1.99-2.0913.80.1986910.9810.9950.0580.2071.863100
2.09-2.2213.20.186980.9810.9950.0550.1882.26999.4
2.22-2.39120.1577040.9830.9960.0510.1662.63899.6
2.39-2.63110.1336880.9750.9940.0460.1422.62898.9
2.63-3.0212.80.1177220.9920.9980.0360.1223.293100
3.02-3.811.80.0967260.9940.9980.030.1013.51299.9
3.8-5011.50.0877790.9940.9990.0270.0913.1499.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.04 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.328 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20764 630 4.6 %RANDOM
Rwork0.16196 ---
obs0.16416 12941 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.478 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.3 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.4→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms595 0 32 54 681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012731
X-RAY DIFFRACTIONr_bond_other_d0.0010.016658
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.8121009
X-RAY DIFFRACTIONr_angle_other_deg0.5141.8141504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.502511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17410117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02946
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3211.989339
X-RAY DIFFRACTIONr_mcbond_other5.2321.986339
X-RAY DIFFRACTIONr_mcangle_it7.7863.569436
X-RAY DIFFRACTIONr_mcangle_other7.7923.577437
X-RAY DIFFRACTIONr_scbond_it6.3452.233392
X-RAY DIFFRACTIONr_scbond_other6.3362.233392
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4023.979574
X-RAY DIFFRACTIONr_long_range_B_refined13.44421.46791
X-RAY DIFFRACTIONr_long_range_B_other12.88920.92779
X-RAY DIFFRACTIONr_rigid_bond_restr3.34631389
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.433 Å
RfactorNum. reflection% reflection
Rfree0.425 40 -
Rwork0.294 710 -
obs--74.78 %

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