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- PDB-3rco: Crystal structure of a conserved motif in human TDRD7 -

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Basic information

Entry
Database: PDB / ID: 3rco
TitleCrystal structure of a conserved motif in human TDRD7
ComponentsTudor domain-containing protein 7
KeywordsDNA BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / HLH motif
Function / homology
Function and homology information


ribonucleoprotein granule / lens morphogenesis in camera-type eye / : / chromatoid body / lens fiber cell differentiation / post-transcriptional regulation of gene expression / spermatogenesis / mitochondrial matrix / mRNA binding / cytoplasm
Similarity search - Function
TDRD7, third LOTUS domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain ...TDRD7, third LOTUS domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SNase-like, OB-fold superfamily / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tudor domain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDong, A. / Xu, C. / Walker, J.R. / Lam, R. / Guo, Y. / Bian, C. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Dong, A. / Xu, C. / Walker, J.R. / Lam, R. / Guo, Y. / Bian, C. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of a conserved motif in human TDRD7
Authors: Xu, C. / Dong, A. / Walker, J.R. / Lam, R. / Guo, Y. / Bian, C. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tudor domain-containing protein 7
B: Tudor domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,37513
Polymers19,9852
Non-polymers39011
Water3,171176
1
B: Tudor domain-containing protein 7
hetero molecules
x 12
A: Tudor domain-containing protein 7
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)244,500156
Polymers239,82024
Non-polymers4,680132
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_444x-1/2,y-1/2,z-1/21
crystal symmetry operation14_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation15_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation16_455x-1/2,-y+1/2,-z+1/21
crystal symmetry operation17_444z-1/2,x-1/2,y-1/21
crystal symmetry operation18_455z-1/2,-x+1/2,-y+1/21
crystal symmetry operation19_554-z+1/2,-x+1/2,y-1/21
crystal symmetry operation20_545-z+1/2,x-1/2,-y+1/21
crystal symmetry operation21_444y-1/2,z-1/2,x-1/21
crystal symmetry operation22_545-y+1/2,z-1/2,-x+1/21
crystal symmetry operation23_455y-1/2,-z+1/2,-x+1/21
crystal symmetry operation24_554-y+1/2,-z+1/2,x-1/21
Buried area66610 Å2
ΔGint-1505 kcal/mol
Surface area64790 Å2
MethodPISA
2
B: Tudor domain-containing protein 7
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)123,313108
Polymers119,91012
Non-polymers3,40396
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area31970 Å2
ΔGint-951 kcal/mol
Surface area37800 Å2
MethodPISA
3
A: Tudor domain-containing protein 7
hetero molecules

A: Tudor domain-containing protein 7
hetero molecules

A: Tudor domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,29712
Polymers29,9773
Non-polymers3199
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area3990 Å2
ΔGint-110 kcal/mol
Surface area11420 Å2
MethodPISA
4
B: Tudor domain-containing protein 7
hetero molecules

B: Tudor domain-containing protein 7
hetero molecules

B: Tudor domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,82827
Polymers29,9773
Non-polymers85124
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6810 Å2
ΔGint-312 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.788, 99.788, 99.788
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-8-

CL

21A-102-

HOH

31A-104-

HOH

41B-6-

HOH

51B-101-

HOH

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Components

#1: Protein Tudor domain-containing protein 7 / PCTAIRE2-binding protein / Tudor repeat associator with PCTAIRE 2 / Trap


Mass: 9992.499 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD7, PCTAIRE2BP / Plasmid: pet28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon plus RIL / References: UniProt: Q8NHU6
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M NaOAc, 2.2-2.4M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2010 / Details: Si 111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 15460 / Num. obs: 15460 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.3 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 47.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 8.75 / Num. unique all: 1500 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SOLVEphasing
REFMAC5.5.0102refinement
Coot0.6model building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.671 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23024 1180 7.6 %RANDOM
Rwork0.17364 ---
all0.17794 15460 --
obs0.17794 14272 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.087 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 11 176 1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9811676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.0321.83749
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63615207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8781513
X-RAY DIFFRACTIONr_chiral_restr0.1110.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021929
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.6291.5786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.78421263
X-RAY DIFFRACTIONr_scbond_it3.6333448
X-RAY DIFFRACTIONr_scangle_it5.514.5413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 88 -
Rwork0.204 1035 -
obs--99.91 %

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