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- PDB-4zb3: Crystal structure of the apo AtNUDT7 -

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Basic information

Entry
Database: PDB / ID: 4zb3
TitleCrystal structure of the apo AtNUDT7
ComponentsNudix hydrolase 7
KeywordsHYDROLASE / Nudix / apo / open 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 / 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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Nudix hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2882
Polymers35,1921
Non-polymers961
Water1,838102
1
A: Nudix hydrolase 7
hetero molecules

A: Nudix hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5764
Polymers70,3842
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area8720 Å2
ΔGint-100 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.788, 116.788, 115.735
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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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.: 1
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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.7 Å3/Da / Density % sol: 66.53 %
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: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21343 / % possible obs: 99.4 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.083 / Χ2: 0.989 / Net I/av σ(I): 24.788 / Net I/σ(I): 11.7 / Num. measured all: 220678
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.3810.50.49120820.706100
2.38-2.4810.60.35220950.739100
2.48-2.5910.70.27921010.766100
2.59-2.7310.70.20721150.806100
2.73-2.910.60.14721140.879100
2.9-3.1210.60.11221250.959100
3.12-3.4410.50.09121401.083100
3.44-3.9310.30.09321471.53299.9
3.93-4.959.70.08821411.88597.7
4.95-509.30.03722830.57997

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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: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.783 / SU ML: 0.121 / Cross valid method: FREE R-VALUE / ESU R: 0.205 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22593 1095 5.2 %RANDOM
Rwork0.19895 ---
obs0.20029 20119 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.88 Å2 / Biso mean: 43.043 Å2 / Biso min: 23.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 5 102 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022143
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9492905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38225.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98715379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.801157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211605
LS refinement shellResolution: 2.291→2.351 Å
RfactorNum. reflection% reflection
Rfree0.248 78 -
Rwork0.26 1243 -
obs--95.45 %

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