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- PDB-5iw5: Crystal structure of E. coli NudC in complex with NMN -

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Basic information

Entry
Database: PDB / ID: 5iw5
TitleCrystal structure of E. coli NudC in complex with NMN
ComponentsNADH pyrophosphatase
KeywordsHYDROLASE / NMN / RNA / capping / Nudix
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
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NAD-capped RNA hydrolase NudC / NAD-capped RNA hydrolase NudC
Similarity search - Component
Biological speciesEscherichia coli B354 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, S. / Du, J. / Patel, D.J.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structure and function of the bacterial decapping enzyme NudC
Authors: Hofer, K. / Li, S. / Abele, F. / Frindert, J. / Schlotthauer, J. / Grawenhoff, J. / Du, J. / Patel, D.J. / Jaschke, A.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Nov 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
B: NADH pyrophosphatase
A: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4256
Polymers59,6242
Non-polymers8014
Water2,000111
1
B: NADH pyrophosphatase
hetero molecules

B: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4256
Polymers59,6242
Non-polymers8014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area2600 Å2
ΔGint-17 kcal/mol
Surface area25520 Å2
MethodPISA
2
A: NADH pyrophosphatase
hetero molecules

A: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4256
Polymers59,6242
Non-polymers8014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,y,-z1
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.863, 62.218, 86.877
Angle α, β, γ (deg.)90.00, 94.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-403-

HOH

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Components

#1: Protein NADH pyrophosphatase / NudC


Mass: 29812.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli B354 (bacteria) / Strain: B354 / Gene: nudC / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: D6JHV3, UniProt: P32664*PLUS, 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-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1 M LiCl2, 0.1 M HEPES, 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15413 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.81 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VK6

1vk6


Resolution: 2.7→46.55 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1
RfactorNum. reflection% reflection
Rfree0.235 770 5.01 %
Rwork0.196 --
obs0.198 15382 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 46 111 4287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144280
X-RAY DIFFRACTIONf_angle_d1.4845822
X-RAY DIFFRACTIONf_dihedral_angle_d19.0131582
X-RAY DIFFRACTIONf_chiral_restr0.229616
X-RAY DIFFRACTIONf_plane_restr0.005752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.90850.30831520.26852889X-RAY DIFFRACTION99
2.9085-3.20110.27671400.23962896X-RAY DIFFRACTION99
3.2011-3.66420.28721740.20292889X-RAY DIFFRACTION99
3.6642-4.61580.18521420.15972942X-RAY DIFFRACTION100
4.6158-46.55260.20961620.18632996X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83030.77642.01062.7819-0.10075.51270.04090.19530.01890.31260.0184-0.0769-0.4108-0.0682-0.0590.32730.03130.04910.16620.0180.2117145.465826.044525.2093
22.78781.18220.05652.6280.27123.5669-0.0633-0.04860.04540.2423-0.01090.5494-0.052-0.70590.04590.36160.08460.04720.387500.2475140.30683.056243.5937
32.5252-0.8041-1.65922.6980.16033.76710.0239-0.2361-0.18780.3021-0.07520.01860.19580.11440.02070.183-0.0226-0.01410.21030.01590.2092146.271650.365916.4623
42.4832-1.3157-0.2982.14760.1351.29780.120.173-0.1316-0.1755-0.15330.2356-0.1073-0.03670.0320.138-0.01060.00310.22760.01210.1914145.02573.6647-2.947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 2 THROUGH 116 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 117 THROUGH 257 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 1 THROUGH 115 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 116 THROUGH 257 )

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