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- PDB-8zb3: Crystal structure of NudC from Mycobacterium abscessus -

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Basic information

Entry
Database: PDB / ID: 8zb3
TitleCrystal structure of NudC from Mycobacterium abscessus
ComponentsNAD(+) diphosphatase
KeywordsHYDROLASE / NudC / Nudix / phosphohydrolases
Function / homology
Function and homology information


NADP+ catabolic process / NAD+ diphosphatase / NADH pyrophosphatase activity / NAD+ catabolic process / : / metal ion binding / cytosol
Similarity search - Function
NADH pyrophosphatase-like, N-terminal / NADH pyrophosphatase-like rudimentary NUDIX domain / Zinc ribbon, NADH pyrophosphatase / : / NADH pyrophosphatase zinc ribbon domain / : / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. ...NADH pyrophosphatase-like, N-terminal / NADH pyrophosphatase-like rudimentary NUDIX domain / 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
IMIDAZOLE / NAD(+) diphosphatase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMeng, L. / Zhang, Y. / Xu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentSKLRD-Z-202415 China
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Studies on Mycobacterial NudC Reveal a Class of Zinc Independent NADH Pyrophosphatase.
Authors: Meng, L. / Sun, Z. / Zhang, Y. / Dong, Y. / Du, X. / Wu, Y. / Yuan, Y. / Sun, Y. / Xu, Y. / Ding, H. / Liu, J. / Xu, J.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(+) diphosphatase
B: NAD(+) diphosphatase
C: NAD(+) diphosphatase
D: NAD(+) diphosphatase
E: NAD(+) diphosphatase
F: NAD(+) diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,43223
Polymers208,7216
Non-polymers71017
Water5,134285
1
A: NAD(+) diphosphatase
B: NAD(+) diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7747
Polymers69,5742
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-70 kcal/mol
Surface area24630 Å2
MethodPISA
2
C: NAD(+) diphosphatase
F: NAD(+) diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7346
Polymers69,5742
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-56 kcal/mol
Surface area25040 Å2
MethodPISA
3
D: NAD(+) diphosphatase
E: NAD(+) diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,92310
Polymers69,5742
Non-polymers3508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-79 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.009, 133.549, 118.730
Angle α, β, γ (deg.)90.00, 95.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NAD(+) diphosphatase


Mass: 34786.914 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: nudC, D2E76_25755, ERS075579_02720, ERS075604_04155 / Production host: Escherichia (bacteria) / References: UniProt: A0A0U1C370, NAD+ diphosphatase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG8000, 0.1 M imidazole pH 8.0, 0.2 M Ca(OAc)2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→39.82 Å / Num. obs: 84252 / % possible obs: 99.2 % / Redundancy: 6.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Χ2: 0.72 / Net I/σ(I): 9.4 / Num. measured all: 534605
Reflection shellResolution: 2.2→2.24 Å / % possible obs: 98.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.925 / Num. measured all: 29284 / Num. unique obs: 4455 / CC1/2: 0.944 / Rpim(I) all: 0.397 / Rrim(I) all: 1.01 / Χ2: 0.77 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
MOLREPphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.244 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22931 4224 5 %RANDOM
Rwork0.19681 ---
obs0.19845 80023 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.367 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20.73 Å2
2---2.45 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.2→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13097 0 21 285 13403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213400
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612614
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.63818220
X-RAY DIFFRACTIONr_angle_other_deg0.4541.57528903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24251682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2435140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.292102048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.21989
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1764.4496791
X-RAY DIFFRACTIONr_mcbond_other4.1764.4496791
X-RAY DIFFRACTIONr_mcangle_it6.0677.9768452
X-RAY DIFFRACTIONr_mcangle_other6.0667.9768453
X-RAY DIFFRACTIONr_scbond_it4.8545.0016609
X-RAY DIFFRACTIONr_scbond_other4.8535.0016610
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4318.9289769
X-RAY DIFFRACTIONr_long_range_B_refined9.57347.9314406
X-RAY DIFFRACTIONr_long_range_B_other9.5847.9714370
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 311 -
Rwork0.299 5916 -
obs--98.61 %

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