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- PDB-3nuq: Structure of a putative nucleotide phosphatase from Saccharomyces... -

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Basic information

Entry
Database: PDB / ID: 3nuq
TitleStructure of a putative nucleotide phosphatase from Saccharomyces cerevisiae
Componentsputative nucleotide phosphatase
KeywordsHYDROLASE / SUPPRESSES THE 6-AU SENSITIVITY OF TRANSCRIPTION ELONGATION FACTOR S-II / RESISTANCE TO PYRIMIDINE DERIVATIVES / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / alpha-beta hydrolase / PYRIMIDINE NUCLEOTIDASE / metal dependent
Function / homology
Function and homology information


nucleotidase activity / pyrimidine nucleobase metabolic process / nucleotide catabolic process
Similarity search - Function
DNA polymerase; domain 1 - #450 / Pyrimidine 5-nucleotidase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...DNA polymerase; domain 1 - #450 / Pyrimidine 5-nucleotidase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Suppressor of disruption of TFIIS
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsDong, A. / Yang, C. / Singer, A.U. / Evdokimova, E. / Kudritsdka, M. / Brown, G. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a putative nucleotide phosphatase from Saccharomyces cerevisiae
Authors: Brown, G. / Evdokimova, E. / Kudritska, M. / Dong, A. / Yang, C. / Singer, A.U. / Edwards, A.M. / Savchenko, A. / Yakunin, A.F.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative nucleotide phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5287
Polymers32,2041
Non-polymers3246
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.474, 64.664, 67.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein putative nucleotide phosphatase / Protein SSM1


Mass: 32203.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TEV cleavage
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: SDT1, SSM1, YGL224C / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: P53078, 5'-nucleotidase

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH6.5, 25 PEG 2K MME (monomethyl ether) cryoprotected with 25% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Feb 15, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→23.38 Å / Num. all: 34511 / % possible obs: 95.5 % / Observed criterion σ(F): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 14.95
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.7 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHELXCDphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: Cr dataset at wavelength of 2.27 A, with a Rigaku MicroMax-007 HF generator and a Cr Raxis4++ detector. This was subsequently refined using a Cu-wavelength dataset deposited here.

Resolution: 1.7→23.38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.066 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22611 2889 10 %RANDOM
Rwork0.19395 ---
obs0.19722 25924 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.81 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 18 140 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222286
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9763099
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93924.717106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91615419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021713
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21034
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21572
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7731.51387
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42722258
X-RAY DIFFRACTIONr_scbond_it2.4083915
X-RAY DIFFRACTIONr_scangle_it3.9524.5836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 189 -
Rwork0.295 1835 -
obs--97.4 %

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