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- PDB-7e44: Crystal structure of NudC complexed with dpCoA -

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Basic information

Entry
Database: PDB / ID: 7.0E+44
TitleCrystal structure of NudC complexed with dpCoA
ComponentsNADH pyrophosphatase
KeywordsHYDROLASE / NudC / dpCoA.
Function / homology
Function and homology information


NAD+ diphosphatase / NAD+ diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / manganese ion binding / magnesium ion binding / zinc ion binding
Similarity search - Function
NAD-capped RNA hydrolase NudC / Zinc ribbon, NADH pyrophosphatase / NADH pyrophosphatase zinc ribbon 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
DEPHOSPHO COENZYME A / NAD-capped RNA hydrolase NudC
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, W. / Guan, Z.Y. / Yin, P. / Zhang, D.L.
CitationJournal: Rna Biol. / Year: 2021
Title: Structural insights into dpCoA-RNA decapping by NudC.
Authors: Zhou, W. / Guan, Z. / Zhao, F. / Ye, Y. / Yang, F. / Yin, P. / Zhang, D.
History
DepositionFeb 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,36910
Polymers119,7334
Non-polymers1,6376
Water10,845602
1
A: NADH pyrophosphatase
B: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9974
Polymers59,8662
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: NADH pyrophosphatase
F: NADH pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3726
Polymers59,8662
Non-polymers1,5064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.837, 61.651, 93.893
Angle α, β, γ (deg.)97.243, 100.386, 111.139
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 12 through 255)
d_2ens_1(chain "B" and (resid 12 through 254 or (resid 255...
d_3ens_1(chain "E" and resid 12 through 255)
d_4ens_1(chain "F" and (resid 12 through 254 or (resid 255...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TRPGLUA12 - 255
d_21ens_1TRPGLUC1 - 244
d_31ens_1TRPGLUE13 - 256
d_41ens_1TRPGLUH13 - 256

NCS oper:
IDCodeMatrixVector
1given(-0.0507335736566, -0.518039904513, 0.853850550059), (-0.603952165372, -0.664994884955, -0.439344494589), (0.795404228331, -0.537974404889, -0.279133755103)-15.4806558869, -2.82208517984, 18.9613570508
2given(0.0967255739254, -0.697940794744, 0.709593412019), (-0.612595502479, -0.603647844206, -0.510231350005), (0.784455807354, -0.385341312627, -0.485943576036)4.16760883788, -21.666394355, -25.0365164561
3given(0.973611641882, 0.142840294707, 0.17798039499), (-0.128333890497, 0.987586640778, -0.0905706326968), (-0.188708196278, 0.065339705885, 0.979857101568)16.5510164285, -19.4534015131, -45.0355234674

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Components

#1: Protein
NADH pyrophosphatase


Mass: 29933.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Gene: nudC, ECBD_4036, HO396_19860 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A140SS78, NAD+ diphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H35N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: PEG 3350, Ammonium succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→90.33 Å / Num. obs: 80253 / % possible obs: 97 % / Redundancy: 1.8 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.051 / Rrim(I) all: 0.072 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 5889 / CC1/2: 0.976 / Rpim(I) all: 0.101 / Rrim(I) all: 0.143

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ISY

5isy


Resolution: 2→90.33 Å / SU ML: 0.2539 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 3998 4.99 %
Rwork0.234 76133 -
obs0.2347 80131 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.8 Å2
Refinement stepCycle: LAST / Resolution: 2→90.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8229 0 92 602 8923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01418544
X-RAY DIFFRACTIONf_angle_d1.407211620
X-RAY DIFFRACTIONf_chiral_restr0.0861213
X-RAY DIFFRACTIONf_plane_restr0.01361502
X-RAY DIFFRACTIONf_dihedral_angle_d13.23123182
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.54610528972
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.66332318119
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.6532206899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.34861240.28482578X-RAY DIFFRACTION95.07
2.02-2.050.27891310.27652658X-RAY DIFFRACTION96.24
2.05-2.070.34521260.28422567X-RAY DIFFRACTION96.08
2.07-2.10.32151150.27462656X-RAY DIFFRACTION96.22
2.1-2.130.27381360.26672593X-RAY DIFFRACTION96.13
2.13-2.160.2881650.27572614X-RAY DIFFRACTION96.39
2.16-2.190.27531360.27662620X-RAY DIFFRACTION96.53
2.19-2.230.32741470.26332565X-RAY DIFFRACTION96.68
2.23-2.260.30321420.26962627X-RAY DIFFRACTION96.62
2.26-2.30.27131500.26532561X-RAY DIFFRACTION94.76
2.3-2.340.28031220.27562644X-RAY DIFFRACTION95.98
2.34-2.390.29781310.27322609X-RAY DIFFRACTION96.79
2.39-2.440.28661270.26582626X-RAY DIFFRACTION97.31
2.44-2.490.28661230.27072646X-RAY DIFFRACTION96.92
2.49-2.550.28911350.25942650X-RAY DIFFRACTION97.34
2.55-2.610.28711500.25932576X-RAY DIFFRACTION96.33
2.61-2.680.25941460.26392660X-RAY DIFFRACTION97.33
2.68-2.760.27861350.25662654X-RAY DIFFRACTION97.21
2.76-2.850.27971560.25462580X-RAY DIFFRACTION96.85
2.85-2.950.25171290.25862646X-RAY DIFFRACTION97.33
2.95-3.070.25881380.25562641X-RAY DIFFRACTION98.13
3.07-3.210.27551380.23812709X-RAY DIFFRACTION98.14
3.21-3.380.24431260.24142660X-RAY DIFFRACTION97.86
3.38-3.590.21831190.22712620X-RAY DIFFRACTION96.24
3.59-3.870.21681380.212687X-RAY DIFFRACTION98.71
3.87-4.260.22911570.19172645X-RAY DIFFRACTION98.91
4.26-4.880.17231260.17462680X-RAY DIFFRACTION98.59
4.88-6.140.22441620.2062671X-RAY DIFFRACTION98.88
6.14-90.330.22691680.22032490X-RAY DIFFRACTION93.3
Refinement TLS params.Method: refined / Origin x: 2.02178554241 Å / Origin y: -11.9390956206 Å / Origin z: -13.4275061816 Å
111213212223313233
T0.196162846467 Å2-0.0197093721484 Å2-0.0197211403714 Å2-0.189179835884 Å20.0377211604076 Å2--0.221584782014 Å2
L0.481043153505 °2-0.0662926302667 °2-0.0680540948974 °2-0.443698700317 °20.190019893655 °2--0.588302644263 °2
S0.0533073323042 Å °-0.0459532836084 Å °-0.00985869803754 Å °0.0781835482632 Å °-0.0242493824115 Å °-0.0527638654008 Å °0.0488822735365 Å °-0.0325183128802 Å °-0.0301709094262 Å °
Refinement TLS groupSelection details: all

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