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- PDB-4zbp: Crystal structure of the AMPCPR-bound AtNUDT7 -

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Basic information

Entry
Database: PDB / ID: 4zbp
TitleCrystal structure of the AMPCPR-bound AtNUDT7
ComponentsNudix hydrolase 7
KeywordsHYDROLASE / Nudix / AMPCPR / closed conformation
Function / homology
Function and homology information


NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / NAD binding / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Nudix hydrolase 6-like / Pre-nudix hydrolase domain / Nudix hydrolase domain / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
ALPHA-BETA METHYLENE ADP-RIBOSE / Nudix hydrolase 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTang, Q. / Liu, C. / Zhong, C. / Ding, J.
CitationJournal: Mol Plant / Year: 2015
Title: Crystal Structures of Arabidopsis thaliana Nudix Hydrolase NUDT7 Reveal a Previously Unobserved Conformation.
Authors: Tang, Q. / Liu, C. / Zhong, C. / Ding, J.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 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 / pdbx_struct_special_symmetry
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: Nudix hydrolase 7
B: Nudix hydrolase 7
C: Nudix hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5178
Polymers105,5753
Non-polymers9425
Water1,62190
1
A: Nudix hydrolase 7
B: Nudix hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6725
Polymers70,3842
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-88 kcal/mol
Surface area26020 Å2
MethodPISA
2
C: Nudix hydrolase 7
hetero molecules

C: Nudix hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6906
Polymers70,3842
Non-polymers1,3074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8790 Å2
ΔGint-72 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.202, 258.720, 157.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-523-

HOH

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Components

#1: Protein Nudix hydrolase 7 / / AtNUDT7 / ADP-ribose pyrophosphatase / NADH pyrophosphatase / Protein GROWTH FACTOR GENE 1


Mass: 35191.793 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NUDT7, GFG1, NUDX7, At4g12720, T20K18.70 / Plasmid: pSJ2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus
References: UniProt: Q9SU14, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, ADP-ribose diphosphatase, NAD+ diphosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADV / ALPHA-BETA METHYLENE ADP-RIBOSE / AMPCPR / {[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-(3,4,5-TRIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL) ESTER


Mass: 557.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O13P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.73 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M NaCl, 0.1 M HEPES, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 30194 / % possible obs: 96.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Χ2: 1.471 / Net I/av σ(I): 28.705 / Net I/σ(I): 15.8 / Num. measured all: 113718
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.693.80.48730361.46498.3
2.69-2.83.80.35929961.44597.8
2.8-2.933.80.24830171.498
2.93-3.083.80.16830121.47197.9
3.08-3.283.80.11130101.4597.5
3.28-3.533.80.06430201.34497.1
3.53-3.883.80.04230241.2696.8
3.88-4.443.80.03830171.78995.8
4.44-5.63.70.03729801.71494.5
5.6-403.70.02530821.38292.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZB3

4zb3


Resolution: 2.6→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.28978 1519 -Random
Rwork0.23796 ---
obs0.2405 28567 96.5 %-
Displacement parametersBiso max: 144.7 Å2 / Biso mean: 59.9812 Å2 / Biso min: 30.36 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 56 90 6428

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