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- PDB-3e2v: Crystal structure of an uncharacterized amidohydrolase from Sacch... -

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Basic information

Entry
Database: PDB / ID: 3e2v
TitleCrystal structure of an uncharacterized amidohydrolase from Saccharomyces cerevisiae
Components3'-5'-exonuclease
KeywordsHYDROLASE / STRUCTURAL GENOMICS / Exonuclease / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


endodeoxyribonuclease activity, producing 5'-phosphomonoesters / exonuclease activity
Similarity search - Function
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized amidohydrolase from Saccharomyces cerevisiae
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: 3'-5'-exonuclease
B: 3'-5'-exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3049
Polymers90,8632
Non-polymers4417
Water12,683704
1
A: 3'-5'-exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6404
Polymers45,4311
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3'-5'-exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6645
Polymers45,4311
Non-polymers2334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.532, 55.007, 115.260
Angle α, β, γ (deg.)90.000, 95.850, 90.000
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological unit is probable monomer

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Components

#1: Protein 3'-5'-exonuclease


Mass: 45431.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: SCY_0164 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6ZKP4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 9
Details: 100mM Tris HCl pH 9, 32% PEG 4K, 200mM magnesium chloride hexahydrate, pH 9.0, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 2, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.5→114.708 Å / Num. all: 124867 / Num. obs: 123244 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 13.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.6 / Num. measured all: 116098 / Num. unique all: 17650 / Rsym value: 0.413 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.887 / SU B: 1.112 / SU ML: 0.043 / SU R Cruickshank DPI: 0.071 / SU Rfree: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 6190 5 %RANDOM
Rwork0.173 ---
obs0.174 123161 98.73 %-
all-124745 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.51 Å2 / Biso mean: 20.729 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.18 Å2
2--0.01 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5793 0 27 704 6524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225998
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9648119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3655741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15624.71276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3381523
X-RAY DIFFRACTIONr_chiral_restr0.0870.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024475
X-RAY DIFFRACTIONr_nbd_refined0.1980.22917
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2541
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.230
X-RAY DIFFRACTIONr_mcbond_it0.8411.53755
X-RAY DIFFRACTIONr_mcangle_it1.36625907
X-RAY DIFFRACTIONr_scbond_it2.31432521
X-RAY DIFFRACTIONr_scangle_it3.3614.52201
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 455 -
Rwork0.188 8395 -
all-8850 -
obs-8395 97.18 %

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