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- PDB-2oie: Crystal structure of RS21-C6 core segment RSCUT -

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Basic information

Entry
Database: PDB / ID: 2oie
TitleCrystal structure of RS21-C6 core segment RSCUT
ComponentsRS21-C6
KeywordsHYDROLASE / HELIX
Function / homology
Function and homology information


dCTP catabolic process / pyrimidine deoxyribonucleotide binding / dCTP diphosphatase / dCTP diphosphatase activity / nucleoside triphosphate catabolic process / pyrophosphatase activity / nucleoside triphosphate diphosphatase activity / DNA protection / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
dCTP pyrophosphatase 1 / : / MazG-like family / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
dCTP pyrophosphatase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.2 Å
AuthorsWu, B. / Liu, Y. / Zhao, Q. / Liao, S. / Zhang, J. / Bartlam, M. / Chen, W. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of RS21-C6, Involved in Nucleoside Triphosphate Pyrophosphohydrolysis
Authors: Wu, B. / Liu, Y. / Zhao, Q. / Liao, S. / Zhang, J. / Bartlam, M. / Chen, W. / Rao, Z.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: RS21-C6
B: RS21-C6
C: RS21-C6
D: RS21-C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0539
Polymers50,5734
Non-polymers4805
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint-189 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.204, 62.616, 137.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer generated from the two dimers in one asymmetric unit.

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Components

#1: Protein
RS21-C6 / RIKEN cDNA 2410015N17 gene / ES cells cDNA / RIKEN full-length enriched library / clone:2410029L09 ...RIKEN cDNA 2410015N17 gene / ES cells cDNA / RIKEN full-length enriched library / clone:2410029L09 product:RS21-C6 homolog / ES cells cDNA / RIKEN full-length enriched library / clone:2410015N17 product:hypothetical protein / full insert sequence / 18-day embryo whole body cDNA / RIKEN full-length enriched library / clone:1110012M04 product:RS21-C6 2410015N17RIK PROTEIN / RIKEN CDNA 2410015N17 GENE / full insert sequence / RSCUT


Mass: 12643.281 Da / Num. of mol.: 4 / Fragment: core segment, residues 21-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QY93
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2M Lithium Sulfate, 10% iso-Propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 24115 / Num. obs: 24067 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CNSrefinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→30.41 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 --RANDOM
Rwork0.218 ---
all-24127 --
obs-23065 95.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å20 Å2
2---0.9 Å20 Å2
3---3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 25 346 3728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008549
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37356
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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