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- PDB-5iw4: Crystal structure of E. coli NudC in complex with NAD -

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Basic information

Entry
Database: PDB / ID: 5iw4
TitleCrystal structure of E. coli NudC in complex with NAD
ComponentsNADH pyrophosphatase
KeywordsHYDROLASE / NAD / 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 / mRNA catabolic 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 / manganese ion binding / magnesium ion binding / protein homodimerization activity / zinc ion binding
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase - #20 / NAD-capped RNA hydrolase NudC / Zinc ribbon, NADH pyrophosphatase / : / NADH pyrophosphatase zinc ribbon domain / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. ...Nucleoside Triphosphate Pyrophosphohydrolase - #20 / NAD-capped RNA hydrolase NudC / Zinc ribbon, NADH pyrophosphatase / : / NADH pyrophosphatase zinc ribbon domain / : / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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: 2.6 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 1.2Jan 1, 2020Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,0826
Polymers59,6242
Non-polymers1,4584
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-22 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.932, 99.369, 113.655
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 / 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-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.: 136 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium nitrate, 20% PEG3350

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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 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18712 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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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: 2.6→45.53 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.248 958 5.13 %
Rwork0.2 --
obs0.202 18662 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 90 136 4407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114383
X-RAY DIFFRACTIONf_angle_d1.0615968
X-RAY DIFFRACTIONf_dihedral_angle_d16.6521626
X-RAY DIFFRACTIONf_chiral_restr0.075627
X-RAY DIFFRACTIONf_plane_restr0.006762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6007-2.73780.31751450.2492433X-RAY DIFFRACTION99
2.7378-2.90930.26231230.24492508X-RAY DIFFRACTION100
2.9093-3.13390.31991530.23962455X-RAY DIFFRACTION100
3.1339-3.44910.27211220.22222538X-RAY DIFFRACTION100
3.4491-3.9480.24431570.18842512X-RAY DIFFRACTION100
3.948-4.97310.18321320.16162566X-RAY DIFFRACTION100
4.9731-45.53160.24271260.19142692X-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)
17.69381.9594-1.24867.1296-1.61344.258-0.20160.4170.335-0.65250.17560.2387-0.4673-0.08190.2940.48280.0873-0.1120.3387-0.01070.34878.2848-1.1614-53.4731
20.93810.214-2.03014.9231.01168.47470.16460.9368-0.1781-0.6953-0.21381.4935-1.3424-1.62370.09450.53430.1958-0.24490.6558-0.11540.6777-0.9536-4.0638-53.3368
35.51475.2138-1.99637.1969-6.00828.2685-0.05990.13320.4932-1.28370.20110.65690.03890.05930.01760.53430.0785-0.13040.3749-0.12990.322310.3355-2.7727-55.7772
45.5021-1.0748-2.54160.61391.5156.92140.03880.00820.3182-0.1091-0.30940.4784-0.5947-0.82850.21330.30550.0473-0.07240.3488-0.06460.42234.6988-3.2105-46.5524
51.66031.00470.13942.8756-0.56052.5846-0.22320.1693-0.093-0.38240.1463-0.1418-0.3070.26250.08860.28170.01010.01260.2256-0.07780.354621.2169-2.9355-38.981
66.21252.5937-1.68671.9661-0.55466.39230.22790.07390.17460.00810.01470.4027-0.589-0.0016-0.19650.31910.0669-0.04390.2191-0.01470.329918.9841-10.1433-21.1259
70.19050.12061.25713.2371-0.50635.9613-0.0299-0.0367-0.13990.2882-0.02130.11640.09620.01160.02850.12090.03060.02460.31670.03860.379516.5258-15.9103-20.6595
86.3337-2.9904-0.29924.15830.35755.994-0.1296-0.1436-0.76520.1285-0.12920.42520.2796-0.58010.35530.2683-0.0522-0.01930.3989-0.06880.6666.3891-24.2567-22.7588
96.197-0.19450.16526.2556-1.40551.7685-0.3725-0.52680.53240.57730.21460.0675-0.502-0.1270.21680.30380.0115-0.11220.5907-0.1610.51344.39732.879-21.8444
108.1388-1.4857-1.16645.3404-1.21246.7392-0.0998-0.54270.47770.10170.1669-0.4399-0.25440.3377-0.01520.2887-0.0249-0.01120.2863-0.16540.413946.2271-0.0889-19.3526
118.8752-3.2963-1.12724.7042-0.28689.5858-0.1420.270.738-0.1064-0.1903-0.84920.25020.42660.21010.28960.0425-0.02580.4408-0.05160.470448.7981-2.5798-31.1117
123.2314-1.98891.02884.6663-2.44383.7741-0.1045-0.28210.05580.0330.04040.0178-0.1512-0.15410.08270.2394-0.0155-0.03810.2943-0.06360.305331.37514.4315-30.1447
131.9607-2.4482-0.9229.84883.91942.65360.1659-0.0949-0.0439-0.1259-0.12960.20640.0526-0.2739-0.0240.1499-0.0183-0.04030.3580.00360.379428.5961-12.6757-39.3124
142.4839-4.549-1.14488.57121.51794.68510.44680.65890.7701-1.3619-0.177-1.4015-0.5250.5915-0.33670.4382-0.07110.09830.5366-0.04560.46134.6615-16.7766-46.3193
150.5096-0.3715-0.70974.51892.60753.0613-0.06410.1046-0.0155-0.113-0.10480.00610.0908-0.12690.17630.25680.0450.02410.3191-0.01480.381527.83-21.5427-41.5443
169.89312.48910.29498.9293-0.93772.10440.24360.20990.26860.1475-0.139-0.2389-0.87250.0163-0.08550.67210.06560.15540.4079-0.06550.344535.8376-26.4526-53.6246
172.63071.576-0.67576.65812.06386.6568-0.083-0.4766-0.24890.65980.1473-0.32560.07480.2236-0.08450.32980.11210.02060.5275-0.01730.37239.133-31.961-37.2535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 23 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 24 THROUGH 36 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 37 THROUGH 49 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 50 THROUGH 75 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 76 THROUGH 146 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 147 THROUGH 179 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 180 THROUGH 227 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 228 THROUGH 256 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 0 THROUGH 23 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 24 THROUGH 57 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 58 THROUGH 75 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 76 THROUGH 115 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 116 THROUGH 146 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 147 THROUGH 166 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 167 THROUGH 210 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 211 THROUGH 227 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 228 THROUGH 257 )

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