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- PDB-2y1h: Crystal structure of the human TatD-domain protein 3 (TATDN3) -

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Basic information

Entry
Database: PDB / ID: 2y1h
TitleCrystal structure of the human TatD-domain protein 3 (TATDN3)
ComponentsPUTATIVE DEOXYRIBONUCLEASE TATDN3
KeywordsHYDROLASE
Function / homology
Function and homology information


nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleus / metal ion binding
Similarity search - Function
3'-5' ssDNA/RNA exonuclease TatD-like / TatD related DNase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Putative deoxyribonuclease TATDN3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMuniz, J.R.C. / Puranik, S. / Krojer, T. / Yue, W.W. / Ugochukwu, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Muniz, J.R.C. / Puranik, S. / Krojer, T. / Yue, W.W. / Ugochukwu, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Kavanagh, K.L. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Human Tatd-Domain Protein 3 (Tatdn3)
Authors: Muniz, J.R.C. / Puranik, S. / Krojer, T. / Yue, W.W. / Ugochukwu, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Kavanagh, K.L. / Oppermann, U.
History
DepositionDec 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Source and taxonomy ...Database references / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE DEOXYRIBONUCLEASE TATDN3
B: PUTATIVE DEOXYRIBONUCLEASE TATDN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,95211
Polymers60,3212
Non-polymers6319
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-208.5 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.910, 44.910, 233.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.0083, 0.0015), (-0.0083, 0.9996, -0.0254), (-0.0013, -0.0254, -0.9997)
Vector: 27.6965, 0.4529, 23.7332)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PUTATIVE DEOXYRIBONUCLEASE TATDN3 / TATD-DOMAIN PROTEIN 3


Mass: 30160.732 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PL
References: UniProt: Q17R31, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters

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Non-polymers , 5 types, 66 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.26 Å3/Da / Density % sol: 45.53 % / Description: NONE
Crystal growDetails: 0.02M ZN_CL, 20% W/V PEG 6000 AND 10% V/V ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→58.28 Å / Num. obs: 18125 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 64.86 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.89 Å / Cor.coef. Fo:Fc: 0.9474 / Cor.coef. Fo:Fc free: 0.9251 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 921 5.1 %RANDOM
Rwork0.1774 ---
obs0.1795 18070 --
Displacement parametersBiso mean: 68.56 Å2
Baniso -1Baniso -2Baniso -3
1--7.0675 Å20 Å20 Å2
2---7.0675 Å20 Å2
3---14.1351 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 20 57 3986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013988HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.25430HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1831SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes584HARMONIC5
X-RAY DIFFRACTIONt_it3988HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion2.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion537SEMIHARMONIC5
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_contact4772SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2502 152 5.18 %
Rwork0.204 2784 -
all0.2064 2936 -
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)
12.81030.09160.40361.0103-0.42575.7784-0.20430.0510.27570.66-0.06120.4766-0.1992-0.74350.2655-0.07610.19990.02380.044-0.0078-0.173.7464-5.761430.3034
2-0.25960.17820.57950.2923-0.27320.2335-0.01370.00580.03850.01490.0256-0.0451-0.0444-0.0274-0.01190.091-0.1176-0.05880.18740.13260.015324.46033.41140.3236
30.2489-0.1751-0.17953.2858-1.37488.3154-0.1029-0.1781-0.11310.7364-0.2243-0.42310.07440.55630.3272-0.0570.1462-0.09380.06390.0648-0.157417.506-11.808141.0306
41.3077-1.05340.27333.1985-0.75858.3154-0.084-0.043-0.02670.0367-0.2524-0.14240.47930.25820.3365-0.18160.1290.00740.02050.0108-0.130816.0631-15.540622.262
50.70230.3403-1.69260.60690.44858.3154-0.14660.0105-0.2672-0.1795-0.0515-0.2523-0.34180.43110.1981-0.1997-0.0663-0.040.22780.0813-0.117324.6647-6.448-1.833
60.09860.10661.62092.5194-2.42481.8752-0.00630.02890.10040.0046-0.00930.0452-0.02430.04270.01550.18140.17370.04430.06990.1064-0.30414.07975.3133-18.0322
70.29252.5998-2.22253.1198-1.52968.26410.00460.0098-0.2205-0.2425-0.1083-0.2581-0.64650.25520.1037-0.2175-0.05040.02180.1917-0.0159-0.27223.0863-6.1649-16.9287
81.7782-0.67041.8360.1725-0.91752.1526-0.00350.03940.0724-0.04910.0310.1621-0.00250.0418-0.02750.15910.099-0.09610.39580.1105-0.28075.63372.5103-21.4496
96.4768-0.61560.97773.6378-2.79617.2474-0.00060.2089-0.1801-0.74640.15680.08270.2277-0.497-0.1562-0.1194-0.0924-0.01060.3383-0.0878-0.30412.382-12.2445-17.4723
101.24650.77770.24013.07261.68137.8658-0.37760.2925-0.0188-0.22160.24470.2187-0.0486-0.65650.1329-0.2265-0.0541-0.02910.18690.0041-0.13998.3712-12.9952-0.382
110.81391.62893.43285.6544-0.77783.81520.3023-0.0955-0.1056-0.1642-0.4776-0.01180.7418-0.20020.17530.0817-0.04670.0496-0.0349-0.0393-0.165415.7636-22.95970.6469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A4 - A111 )
2X-RAY DIFFRACTION2(A112 - A119 )
3X-RAY DIFFRACTION3(A120 - A189 )
4X-RAY DIFFRACTION4(A190 - A272 )
5X-RAY DIFFRACTION5(B5 - B75 )
6X-RAY DIFFRACTION6(B79 - B85 )
7X-RAY DIFFRACTION7(B86 - B113 )
8X-RAY DIFFRACTION8(B114 - B125 )
9X-RAY DIFFRACTION9(B126 - B175 )
10X-RAY DIFFRACTION10(B176 - B240 )
11X-RAY DIFFRACTION11(B241 - B272 )

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