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- PDB-1vc8: Crystal Structure of a T.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6... -

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Basic information

Entry
Database: PDB / ID: 1vc8
TitleCrystal Structure of a T.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6A Complex
ComponentsNdx1
KeywordsHYDROLASE / Nudix protein / diadenosine polyphosphate / Ap6A / Thermus thermophilus HB8 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / diadenosine hexaphosphate hydrolase (ATP-forming) / ATP biosynthetic process / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP binding / metal ion binding
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 ...: / 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'-PENTAPHOSPHATE / Diadenosine hexaphosphate hydrolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsIwai, T. / Nakagawa, N. / Kuramitsu, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Nudix Protein Ndx1 from Thermus thermophilus HB8 in binary complex with diadenosine hexaphosphate
Authors: Iwai, T. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionMar 5, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ndx1
B: Ndx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7074
Polymers28,3732
Non-polymers1,3342
Water4,270237
1
A: Ndx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8532
Polymers14,1861
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ndx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8532
Polymers14,1861
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.413, 54.775, 111.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ndx1 / MutT/nudix family protein


Mass: 14186.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ndx1 / Plasmid: PET11B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q75UV1
#2: Chemical ChemComp-5FA / ADENOSINE-5'-PENTAPHOSPHATE


Type: RNA linking / Mass: 667.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N5O19P5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 1.0M succinic acid, 1%(w/v) PEG 2000 MME, 4mM Ap6A, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418, 0.9744, 0.9792, 0.9798, 0.9819
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 17, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97441
30.97921
40.97981
50.98191
ReflectionResolution: 2→50 Å / Num. obs: 22476 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 42.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 23.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 729991.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2212 9.9 %RANDOM
Rwork0.195 ---
obs0.195 22254 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.7813 Å2 / ksol: 0.390214 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.93 Å20 Å20 Å2
2---2.46 Å20 Å2
3----4.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 78 237 2317
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 347 9.6 %
Rwork0.19 3261 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2P5A.PARAMP5A.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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