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- PDB-3s93: Crystal structure of conserved motif in TDRD5 -

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Basic information

Entry
Database: PDB / ID: 3s93
TitleCrystal structure of conserved motif in TDRD5
ComponentsTudor domain-containing protein 5
KeywordsTRANSCRIPTION / structural genomics consortium / SGC
Function / homology
Function and homology information


: / pi-body / P granule organization / chromatoid body / spermatid development
Similarity search - Function
TDRD5, second 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 ...TDRD5, second 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsChao, X. / Tempel, W. / Bian, C. / Kania, J. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of conserved motif in TDRD5
Authors: Chao, X. / Tempel, W. / Bian, C. / Kania, J. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tudor domain-containing protein 5
B: Tudor domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)22,72110
Polymers22,7212
Non-polymers08
Water37821
1
A: Tudor domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)11,3604
Polymers11,3601
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tudor domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)11,3606
Polymers11,3601
Non-polymers05
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.940, 43.330, 126.600
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 domain-containing protein 5


Mass: 11360.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD5 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q8NAT2
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5952.54
2
3
Crystal grow
Temperature (K)Crystal-IDDetailsPH range
2911crystal used for final refinement: 1.5 M ammonium phosphate, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 8.5, vapor diffusion, temperature 291K8.5; 7; 6.5
2912Selenomethionyl derivative: 1.5 M ammonium phosphat e, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 7, vapor diffusion, temperature 291K
2913crystal used for preliminary refinement: 25 w/v% PEG-3350, 0.2 M lithium sulfate, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 6.5, vapor diffusion, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU FR-E11.5418
SYNCHROTRONCHESS A120.977
SYNCHROTRONCLSI 08ID-130.97949
Detector
TypeIDDetectorDate
RIGAKU SATURN1CCDApr 18, 2011
ADSC Q210 BINNED2CCDMay 11, 2011
MAR 3003CCDMay 25, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9771
30.979491
ReflectionResolution: 2.28→30 Å / Num. obs: 10833 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.51 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 33.8
Reflection shellResolution: 2.28→2.34 Å / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.8 / % possible all: 76.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.28→27.48 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: BUCCANEER AND ARP/WARP WERE USED FOR AUTOMATED MODEL TRACING. DM WAS USED FOR ADDITIONAL PHASE REFINEMENT. REFMAC AND PHENIX WERE ALSO USED FOR REFINEMENT. COOT WAS USED FOR INTERACTIVE ...Details: BUCCANEER AND ARP/WARP WERE USED FOR AUTOMATED MODEL TRACING. DM WAS USED FOR ADDITIONAL PHASE REFINEMENT. REFMAC AND PHENIX WERE ALSO USED FOR REFINEMENT. COOT WAS USED FOR INTERACTIVE MODEL COMPLETION. THE MOLPROBITY SERVER WAS USED TO EVALUATE MODEL GEOMETRY. ABOUT THE DATA SETS: (NATIVE) DATA SET 1 WAS USED FOR FINAL REFINEMENT. OF THE AVAILABLE DATA SETS, SET ONE EXTENDED TO THE HIGHEST RESOLUTION. HOWEVER, DIFFRACTION IMAGES HAD ICE RINGS AND COMPLETENESS WAS < 95%. DATA SET 2 (P212121; A,B,C = 43.00A,43.56A,126.53A; PROCESSED WITH HKL2000) WAS USED FOR SELENIUM-SAD PHASING. (NATIVE) DATA SET 3 (P212121; A,B,C = 42.83,43.38,126.72A; PROCESSED WITH XDS) IS COMPLETE TO 2.5 A RESOLUTION AND WAS USED DURING INTERMEDIATE STAGES OF MODEL REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 575 5.32 %THIN SHELLS (SFTOOLS)
Rwork0.245 ---
obs0.246 10803 --
Displacement parametersBiso mean: 48.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.5105 Å20 Å20 Å2
2---3.3032 Å20 Å2
3---0.7928 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.28→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 8 21 1226
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011225HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.061661HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d444SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes181HARMONIC5
X-RAY DIFFRACTIONt_it1225HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion17.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion168SEMIHARMONIC5
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_contact1422SEMIHARMONIC4
LS refinement shellResolution: 2.28→2.55 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3058 124 4.24 %
Rwork0.2824 2798 -
all0.2835 2922 -
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)
12.85951.1223-2.3833.5422-0.2457.07880.0408-0.06650.23780.54790.11960.5254-0.0057-0.5269-0.16040.02760.00020.0746-0.16840.0363-0.162714.80158.062829.6696
23.62420.1422-2.32360.9209-0.37114.97530.00850.2356-0.3681-0.2115-0.0282-0.0150.6665-0.1190.0198-0.0317-0.0282-0.0366-0.0416-0.0398-0.169922.00783.6844-0.3128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 79
2X-RAY DIFFRACTION2{ B|* }B0 - 80

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