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- PDB-6ku5: Notothenia coriiceps TRAF5 -

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Basic information

Entry
Database: PDB / ID: 6ku5
TitleNotothenia coriiceps TRAF5
ComponentsTRAF5
KeywordsPROTEIN BINDING / TRAF / Tumor Necrosis Factor Receptor Association Factor / Notothenia coriiceps TRAF5
Function / homologyApoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Sandwich / Mainly Beta
Function and homology information
Biological speciesNotothenia coriiceps (black rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.299 Å
AuthorsPark, H.H. / Kim, C.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Fish Shellfish Immunol. / Year: 2020
Title: Structural and biochemical characterization of TRAF5 from Notothenia coriiceps and its implications in fish immune cell signaling.
Authors: Kim, C.M. / Jang, H. / Ha, H.J. / Kim, G.E. / Park, H.H.
History
DepositionAug 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: TRAF5
B: TRAF5


Theoretical massNumber of molelcules
Total (without water)46,1322
Polymers46,1322
Non-polymers00
Water00
1
A: TRAF5

A: TRAF5

A: TRAF5


Theoretical massNumber of molelcules
Total (without water)69,1993
Polymers69,1993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4960 Å2
ΔGint-52 kcal/mol
Surface area31010 Å2
MethodPISA
2
B: TRAF5

B: TRAF5

B: TRAF5


Theoretical massNumber of molelcules
Total (without water)69,1993
Polymers69,1993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5970 Å2
ΔGint-42 kcal/mol
Surface area32200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.544, 85.544, 148.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein TRAF5


Mass: 23066.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Notothenia coriiceps (black rockcod) / Production host: Escherichia coli (E. coli)

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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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20%(w/v) PEG-6000, 0.1M HEPES pH 7.0, 0.2M Sodium chloride

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.299→42.81 Å / Num. obs: 9935 / % possible obs: 100 % / Redundancy: 18.5 % / Rsym value: 0.201 / Net I/σ(I): 19.16
Reflection shellResolution: 3.299→7.39 Å / Num. unique obs: 639 / Rsym value: 1.704

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.299→42.804 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.225 / SU B: 28.523 / SU ML: 0.47 / Average fsc free: 0.865 / Average fsc work: 0.892 / Cross valid method: FREE R-VALUE / ESU R Free: 0.572
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2865 984 9.908 %
Rwork0.2461 8947 -
all0.25 --
obs-9931 99.769 %
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: 80.209 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å20.031 Å20 Å2
2--0.061 Å2-0 Å2
3----0.198 Å2
Refinement stepCycle: LAST / Resolution: 3.299→42.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 0 0 3052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133118
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172788
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6354236
X-RAY DIFFRACTIONr_angle_other_deg1.5291.5736457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.095406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44423.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73315488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6491512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023546
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02626
X-RAY DIFFRACTIONr_nbd_refined0.2090.2741
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2440.22579
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21576
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4340.231
X-RAY DIFFRACTIONr_nbd_other0.4090.2105
X-RAY DIFFRACTIONr_mcbond_it4.7488.9281630
X-RAY DIFFRACTIONr_mcbond_other4.7248.9281629
X-RAY DIFFRACTIONr_mcangle_it7.34613.3882034
X-RAY DIFFRACTIONr_mcangle_other7.34713.3912035
X-RAY DIFFRACTIONr_scbond_it4.9499.0461488
X-RAY DIFFRACTIONr_scbond_other4.9479.041486
X-RAY DIFFRACTIONr_scangle_it7.57213.4742202
X-RAY DIFFRACTIONr_scangle_other7.57413.4742202
X-RAY DIFFRACTIONr_lrange_it9.675107.2093470
X-RAY DIFFRACTIONr_lrange_other9.674107.2313471
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.299-3.3840.398690.3276280.3337100.7240.78598.1690.303
3.384-3.4760.386670.2736040.2836710.7570.8411000.254
3.476-3.5760.307680.2786230.2816910.8470.8431000.25
3.576-3.6860.357630.2675900.2766530.830.8621000.234
3.686-3.8060.35670.2675890.2756560.8420.8691000.236
3.806-3.9380.263600.2445480.2466080.9080.9041000.206
3.938-4.0850.323570.2385550.2456120.8660.9151000.198
4.085-4.2510.292570.1975160.2075730.9050.9321000.165
4.251-4.4380.205560.1915120.1925680.9240.9351000.168
4.438-4.6520.252530.2134720.2175250.8980.9241000.178
4.652-4.90.279530.2034660.2115190.9030.931000.179
4.9-5.1930.261470.2134360.2174850.9220.94199.58760.187
5.193-5.5460.304450.2434140.254590.9410.9161000.218
5.546-5.9820.343460.2633820.2714280.8180.8911000.235
5.982-6.540.299410.2893690.294100.8540.8761000.257
6.54-7.2910.286370.2823220.2823590.8860.8951000.253
7.291-8.3780.224320.2483090.2463410.9450.9231000.237
8.378-10.1640.205280.2232460.2212740.950.9471000.23
10.164-13.9850.297240.2212190.2272430.9230.9581000.238
13.985-42.8040.321140.3641470.3611610.8260.9041000.372

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