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- PDB-6b57: tudor in complex with ligand -

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Basic information

Entry
Database: PDB / ID: 6b57
Titletudor in complex with ligand
ComponentsTudor and KH domain-containing protein
KeywordsPROTEIN BINDING / tudor domain / protein-binding / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


piP-body / pi-body / P granule organization / piRNA processing / male meiotic nuclear division / P granule / fertilization / PIWI-interacting RNA (piRNA) biogenesis / spermatogenesis / mitochondrion / RNA binding
Similarity search - Function
: / : / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / Type-1 KH domain profile. ...: / : / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / Type-1 KH domain profile. / SNase-like, OB-fold superfamily / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
Tudor and KH domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhang, H. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2.
Authors: Zhang, H. / Liu, K. / Izumi, N. / Huang, H. / Ding, D. / Ni, Z. / Sidhu, S.S. / Chen, C. / Tomari, Y. / Min, J.
History
DepositionSep 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tudor and KH domain-containing protein
B: Tudor and KH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)51,32536
Polymers51,3252
Non-polymers034
Water1,910106
1
A: Tudor and KH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)25,66316
Polymers25,6631
Non-polymers015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tudor and KH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)25,66320
Polymers25,6631
Non-polymers019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.070, 72.660, 130.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tudor and KH domain-containing protein


Mass: 25662.568 Da / Num. of mol.: 2 / Fragment: Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y2W6
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 34 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.18 Å3/Da / Density % sol: 43.51 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG-3350, 0.2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→65.35 Å / Num. obs: 34211 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 15.2 / Num. measured all: 217894 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.93-1.985.20.8251170522300.6470.3870.9161.997.4
9.06-65.355.70.03522353910.9970.0160.03834.798.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.32data reduction
PDB_EXTRACT3.22data extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5j39

5j39


Resolution: 1.93→65.35 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.929 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.14
RfactorNum. reflection% reflection
Rfree0.234 1683 4.92 %
Rwork0.206 --
obs0.208 34210 99 %
Displacement parametersBiso max: 115.34 Å2 / Biso mean: 45.66 Å2 / Biso min: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1-4.2704 Å20 Å20 Å2
2--4.5339 Å20 Å2
3----8.8043 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.93→65.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 34 106 3271
Biso mean--38.31 36.97 -
Num. residues----409
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1058SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes481HARMONIC5
X-RAY DIFFRACTIONt_it3223HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3739SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3223HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4395HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion16.41
LS refinement shellResolution: 1.93→1.99 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.284 139 5.03 %
Rwork0.237 2626 -
all-2765 -
obs--93.53 %
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)
15.26834.23653.98341.49240.50090.2120.007-0.6058-0.21020.43410.1456-0.11510.1892-0.1106-0.1526-0.00020.0055-0.02530.0913-0.046-0.156625.74115.2914-9.3087
202.08132.99035.3972-0.25823.5850.08590.22060.0783-0.20550.0177-0.4606-0.67330.0933-0.1036-0.05060.0220.09360.0769-0.0312-0.085517.59884.8318-26.5047
32.70170.4561.03040.0091.03772.9780.3204-0.5496-0.33360.4418-0.2118-0.14060.5121-0.3493-0.1085-0.0554-0.04680.0075-0.02610.055-0.078111.0449-3.0408-17.7834
400.3569-1.42453.1007-0.99221.81730.1039-0.1121-0.00630.153-0.01350.1053-0.30070.0153-0.0904-0.13560.00040.0278-0.0259-0.07-0.146924.465226.2672-16.5038
54.3425-1.02960.33042.42980.34861.33370.17660.2059-0.303-0.2735-0.32990.3273-0.1354-0.34640.1533-0.16350.06460.0042-0.017-0.0769-0.1346-2.09964.942-29.0506
62.02540.372-0.25723.25631.71013.48480.1159-0.39140.36630.4919-0.0570.3231-0.3168-0.4698-0.05890.05870.10010.1360.148-0.0988-0.13514.407530.0667-1.0078
73.6159-0.11420.14375.35243.55184.14240.2623-0.7215-0.48641.07290.1394-0.52610.9480.0379-0.40160.1042-0.0326-0.13410.02980.1697-0.122716.1677-7.7044-11.6617
81.19960.2843-0.51472.11320.00521.83330.030.05740.0495-0.03980.0563-0.0777-0.19980.0238-0.0863-0.1182-0.01610.03-0.0059-0.0309-0.079529.212826.384-24.8416
90.01465.12541.82780.3594-0.90580-0.0209-0.1292-0.13530.03720.02860.080.01380.0277-0.0078-0.1094-0.1499-0.0076-0.04150.0120.1532.5211-11.1137-21.0643
1000.0958-3.12465.33262.6556.15610.0324-0.0939-0.09590.0125-0.04390.3215-0.3949-0.16830.0115-0.08730.09690.09890.0171-0.03560.02317.810434.4526-13.9874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|300 - A|307 }A300 - 307
2X-RAY DIFFRACTION2{ B|299 - B|307 }B299 - 307
3X-RAY DIFFRACTION3{ A|308 - A|325 }A308 - 325
4X-RAY DIFFRACTION4{ B|308 - B|325 }B308 - 325
5X-RAY DIFFRACTION5{ A|326 - A|418 }A326 - 418
6X-RAY DIFFRACTION6{ B|326 - B|418 }B326 - 418
7X-RAY DIFFRACTION7{ A|419 - A|496 }A419 - 496
8X-RAY DIFFRACTION8{ B|419 - B|495 }B419 - 495
9X-RAY DIFFRACTION9{ A|510 - A|514 }A510 - 514
10X-RAY DIFFRACTION10{ B|511 - B|520 }B511 - 520

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