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- PDB-5isy: Crystal structure of Nudix family protein with NAD -

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Basic information

Entry
Database: PDB / ID: 5isy
TitleCrystal structure of Nudix family protein with NAD
ComponentsNADH pyrophosphatase
KeywordsRNA BINDING PROTEIN / Nudix family / complex / NAD
Function / homology
Function and homology information


: / NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / RNA NAD-cap (NMN-forming) hydrolase activity / NAD-cap decapping / NAD catabolic process / mRNA stabilization / NADH metabolic process ...: / NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / RNA NAD-cap (NMN-forming) hydrolase activity / NAD-cap decapping / NAD catabolic process / mRNA stabilization / NADH metabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisome / manganese ion binding / magnesium ion binding / protein homodimerization activity / zinc ion binding / cytosol
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase - #20 / : / NAD-capped RNA hydrolase NudC / Zinc ribbon, NADH pyrophosphatase / NADH pyrophosphatase zinc ribbon domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain ...Nucleoside Triphosphate Pyrophosphohydrolase - #20 / : / NAD-capped RNA hydrolase NudC / Zinc ribbon, NADH pyrophosphatase / NADH pyrophosphatase zinc ribbon domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-capped RNA hydrolase NudC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.354 Å
AuthorsZhang, D. / Guan, Z. / Zou, T. / Yin, P.
CitationJournal: Cell Res. / Year: 2016
Title: Structural basis of prokaryotic NAD-RNA decapping by NudC
Authors: Zhang, D. / Liu, Y. / Wang, Q. / Guan, Z. / Wang, J. / Liu, J. / Zou, T. / Yin, P.
History
DepositionMar 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH pyrophosphatase
C: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3246
Polymers59,8662
Non-polymers1,4584
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-23 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.411, 98.702, 113.739
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 NADH pyrophosphatase / N6-adenosine-methyltransferase 70 kDa subunit / N6-adenosine-methyltransferase subunit METTL14


Mass: 29933.176 Da / Num. of mol.: 2 / Mutation: E178Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nudC, yjaD, b3996, JW5548 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32664, NAD+ diphosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Sodium Malonate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→45 Å / Num. obs: 25141 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.057 / Rsym value: 0.036 / Net I/σ(I): 25.69
Reflection shellResolution: 2.35→2.44 Å / Rmerge(I) obs: 0.187 / Rsym value: 0.12

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data collection
HKL-3000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GB5

2gb5


Resolution: 2.354→45 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 1241 4.95 %
Rwork0.1822 --
obs0.1852 25085 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.354→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 90 208 4332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084244
X-RAY DIFFRACTIONf_angle_d1.0095790
X-RAY DIFFRACTIONf_dihedral_angle_d20.7672488
X-RAY DIFFRACTIONf_chiral_restr0.056614
X-RAY DIFFRACTIONf_plane_restr0.006741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3544-2.44870.32341460.21882547X-RAY DIFFRACTION98
2.4487-2.56010.28251530.22012598X-RAY DIFFRACTION100
2.5601-2.69510.27751590.21252605X-RAY DIFFRACTION100
2.6951-2.86390.29561180.20022633X-RAY DIFFRACTION100
2.8639-3.0850.28121250.20742656X-RAY DIFFRACTION100
3.085-3.39540.25061180.19492654X-RAY DIFFRACTION100
3.3954-3.88650.23071280.16892666X-RAY DIFFRACTION100
3.8865-4.89570.2031540.14662672X-RAY DIFFRACTION100
4.8957-46.29870.21521400.17122813X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -25.2804 Å / Origin y: 9.4402 Å / Origin z: -34.7879 Å
111213212223313233
T0.1838 Å20.036 Å2-0.0535 Å2-0.2053 Å20.032 Å2--0.1937 Å2
L0.8755 °2-0.0646 °2-0.263 °2-1.0836 °20.0208 °2--0.9349 °2
S-0.1097 Å °0.0086 Å °0.0979 Å °-0.0402 Å °0.0889 Å °-0.0114 Å °-0.0359 Å °-0.0539 Å °0.0333 Å °
Refinement TLS groupSelection details: all

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