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- PDB-1v8r: Crystal structure analysis of the ADP-ribose pyrophosphatase comp... -

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Basic information

Entry
Database: PDB / ID: 1v8r
TitleCrystal structure analysis of the ADP-ribose pyrophosphatase complexed with ADP-ribose and Zn
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / Nudix motif / MutT family / loop-helix-loop / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


pyrophosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / 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
ADENOSINE-5-DIPHOSPHORIBOSE / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYoshiba, S. / Ooga, T. / Nakagawa, N. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
Authors: Yoshiba, S. / Ooga, T. / Nakagawa, N. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / Masui, R.
History
DepositionJan 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)19,9784
Polymers19,2881
Non-polymers6903
Water99155
1
A: ADP-ribose pyrophosphatase
hetero molecules

A: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9568
Polymers38,5762
Non-polymers1,3806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6980 Å2
ΔGint-154 kcal/mol
Surface area12900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.710, 49.710, 118.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsdimer, the second part of the biological assembly is generated by y, x, 1-z.

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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 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q84CU3, ADP-ribose diphosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.29 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1.282 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 16237 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14 Å2 / Rsym value: 0.052
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.096 / % possible all: 99.6

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.02 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 921685.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2924 9.8 %RANDOM
Rwork0.206 ---
obs0.206 29889 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.0493 Å2 / ksol: 0.506776 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å21.42 Å20 Å2
2--1.54 Å20 Å2
3----3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 38 55 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.021.5
X-RAY DIFFRACTIONc_mcangle_it5.12
X-RAY DIFFRACTIONc_scbond_it6.92
X-RAY DIFFRACTIONc_scangle_it7.612.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 518 10.4 %
Rwork0.222 4469 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3APR_XPLOR_PAR.TXTAPR_XPLOR_TOP.TXT
X-RAY DIFFRACTION4ION.PARAMION.TOP

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