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- PDB-2zti: Structures of dimeric nonstandard nucleotide triphosphate pyropho... -

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Basic information

Entry
Database: PDB / ID: 2zti
TitleStructures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes
ComponentsNTPASE
KeywordsHYDROLASE / NTPase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
dITP/XTP pyrophosphatase / Ham1-like protein / Ham1 family / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes
Authors: Lokanath, N.K. / Pampa, K.J. / Takio, K. / Kunishima, N.
History
DepositionOct 6, 2008Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 21, 2008ID: 2EHK
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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: NTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2882
Polymers21,2331
Non-polymers551
Water1,40578
1
A: NTPASE
hetero molecules

A: NTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5774
Polymers42,4672
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2580 Å2
ΔGint-22 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.282, 76.282, 82.585
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NTPASE / Putative uncharacterized protein PH1917


Mass: 21233.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: NTPase, PH1917 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)-RIL
References: UniProt: O59580, nucleoside-triphosphate diphosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.08M MES, 1.6M NH(2)SO4, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 4, 2006 / Details: GRAPHITE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 8895 / Num. obs: 8881 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
EPMRphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V7R

1v7r


Resolution: 2.6→40 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 766 -RANDOM
Rwork0.21 ---
obs0.21 8881 99.8 %-
all-8895 --
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 1 78 1560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.62

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