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- PDB-1xwy: Crystal structure of tatD deoxyribonuclease from Escherichia coli... -

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Basic information

Entry
Database: PDB / ID: 1xwy
TitleCrystal structure of tatD deoxyribonuclease from Escherichia coli K12 at 2.0 A resolution
ComponentsDeoxyribonuclease tatD
KeywordsHYDROLASE / tatD / TIM BARRAEL / deoxyribonuclease / zinc ion / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


DNA nuclease activity / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / response to hydrogen peroxide / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / magnesium ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
3'-5' ssDNA/RNA exonuclease TatD / TatD deoxyribonuclease family signature 2. / TatD deoxyribonuclease family signature 3. / Deoxyribonuclease, TatD-related, conserved site / 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
3'-5' ssDNA/RNA exonuclease TatD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Xiang, D.F. / Raushel, F.M. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of tatD DNase from Escherichia coli at 2.0 A resolution
Authors: Malashkevich, V.N. / Xiang, D.F. / Raushel, F.M. / Almo, S.C.
History
DepositionNov 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 3, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
Revision 1.5Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyribonuclease tatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6522
Polymers29,5871
Non-polymers651
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.885, 73.885, 67.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Deoxyribonuclease tatD / DNase tatD


Mass: 29586.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tatD, mttC / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12
References: UniProt: P27859, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 3.2 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na-HEPES, 1.5 M Lithium Sulfate monohydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 279.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 27, 2004 / Details: mirrors
RadiationMonochromator: Cu-Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 24803 / Num. obs: 22621 / % possible obs: 91.2 % / Observed criterion σ(I): -1.5 / Redundancy: 2.2 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 23.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 10 / Num. unique all: 2048 / Rsym value: 0.447 / % possible all: 84.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J6O

1j6o


Resolution: 2→19.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1427081.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1636 7.2 %RANDOM
Rwork0.171 ---
obs0.171 22601 91.2 %-
all-24621 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8264 Å2 / ksol: 0.30591 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2---1.65 Å20 Å2
3---3.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 1 301 2340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 246 6.9 %
Rwork0.255 3299 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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