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- PDB-8zb4: Crystal structure of NudC from Mycobacterium abscessus in complex... -

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Basic information

Entry
Database: PDB / ID: 8zb4
TitleCrystal structure of NudC from Mycobacterium abscessus in complex with NAD
ComponentsNAD(+) diphosphatase
KeywordsHYDROLASE / NudC / Nudix / pyrophosphatase
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(+) diphosphatase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,42217
Polymers69,5742
Non-polymers1,84815
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-151 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.726, 132.726, 175.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NAD(+) diphosphatase


Mass: 34786.914 Da / Num. of mol.: 2
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 coli (E. coli) / References: UniProt: A0A0U1C370, NAD+ diphosphatase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
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: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 25670 / % possible obs: 99.8 % / Redundancy: 14.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.023 / Rrim(I) all: 0.087 / Χ2: 0.96 / Net I/σ(I): 24 / Num. measured all: 365360
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.908 / Num. measured all: 42020 / Num. unique obs: 3354 / CC1/2: 0.878 / Rpim(I) all: 0.264 / Rrim(I) all: 0.947 / Χ2: 0.88 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
MOLREPphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 25.868 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.567 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26636 1265 4.9 %RANDOM
Rwork0.22188 ---
obs0.22407 24313 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å2-0 Å2
2---0.32 Å2-0 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 101 48 4712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124766
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164396
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.8366505
X-RAY DIFFRACTIONr_angle_other_deg0.5361.7710088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.875591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.247548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97810712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021135
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_it3.7515.8782373
X-RAY DIFFRACTIONr_mcbond_other3.7515.8782373
X-RAY DIFFRACTIONr_mcangle_it6.07210.5632961
X-RAY DIFFRACTIONr_mcangle_other6.07110.5642962
X-RAY DIFFRACTIONr_scbond_it3.8086.4652393
X-RAY DIFFRACTIONr_scbond_other3.8076.4652394
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.39611.713545
X-RAY DIFFRACTIONr_long_range_B_refined11.33170.8918507
X-RAY DIFFRACTIONr_long_range_B_other11.33170.8918508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.493 70 -
Rwork0.344 1751 -
obs--99.89 %
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)
10.40180.24040.0230.2825-0.04960.0311-0.07970.141-0.1010.06540.1027-0.0388-0.05680.0004-0.0230.109-0.02050.03470.0757-0.03080.028810.354151.8064-15.5399
20.59880.23060.1970.110.04320.13730.01430.0023-0.14180.04110.0301-0.0352-0.027-0.0713-0.04440.10060.00050.06590.0816-0.02060.0849-5.900635.6245-8.0271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 301
2X-RAY DIFFRACTION2B2 - 301

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