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- PDB-3x0r: DP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-sta... -

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Basic information

Entry
Database: PDB / ID: 3x0r
TitleDP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-state at reaction time of 30 min
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / Nudix motif / ADP ribose hydrolase / ADP ribose / Cytosol
Function / homology
Function and homology information


pyrophosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / metal ion binding / cytosol
Similarity search - Function
NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsFuruike, Y. / Akita, Y. / Miyahara, I. / Kamiya, N.
CitationJournal: Biochemistry / Year: 2016
Title: ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors
Authors: Furuike, Y. / Akita, Y. / Miyahara, I. / Kamiya, N.
History
DepositionOct 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

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Assembly

Deposited unit
A: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7747
Polymers19,2881
Non-polymers4866
Water2,612145
1
A: ADP-ribose pyrophosphatase
hetero molecules

A: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,54814
Polymers38,5762
Non-polymers97212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6720 Å2
ΔGint-111 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.648, 49.648, 118.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

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Components

#1: Protein ADP-ribose pyrophosphatase


Mass: 19287.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHA0528 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKW5, ADP-ribose diphosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.24M Acetate-Sodium acetate buffer, 0.32M Ammonium sulfate, 30%(w/v) Glycerol, 8%(w/v) PEG 20000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B110.7
SYNCHROTRONSPring-8 BL41XU20.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDFeb 20, 2010
RAYONIX MX-2252CCDJul 4, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Fixed exit Si (111) double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
20.91
ReflectionResolution: 1.15→30 Å / Num. all: 60216 / Num. obs: 60216 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.15-1.171,293.9
1.17-1.191,297.6
1.19-1.211,297.4
1.21-1.241,297.7
1.24-1.271,297.8
1.27-1.31,297.9
1.3-1.331,298.1
1.33-1.361,298.2
1.36-1.41,298.3
1.4-1.451,298.4
1.45-1.51,298.6
1.5-1.561,298.7
1.56-1.631,298.8
1.63-1.721,299
1.72-1.831,299.1
1.83-1.971,299.3
1.97-2.161,299.4
2.16-2.481,299.6
2.48-3.121,299.7
3.12-301,299.3

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0I

3x0i


Resolution: 1.15→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
all0.143 60216
obs0.143 60216
Refinement stepCycle: LAST / Resolution: 1.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 24 145 1375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d2.22

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