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- PDB-9iw1: wild type NMN/NaMN adenylyltransferase from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 9iw1
Titlewild type NMN/NaMN adenylyltransferase from Chaetomium thermophilum
ComponentsNicotinamide-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Adenylyltransferase / Complex
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / ATP binding
Similarity search - Function
Nicotinamide/nicotinate mononucleotide adenylyltransferase, eukaryotic / : / Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / Nicotinamide-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsQian, X.-L. / Zheng, Y.-C. / Chen, C. / Xu, J.-H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Biochemical and structural characterization of a novel nicotinamide mononucleotide adenylyltransferase from thermophilic fungi Chaetomium thermophilum.
Authors: Qian, X.L. / Li, J.Y. / Li, C.X. / Pan, J. / Mu, B. / Xu, J.H.
History
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide-nucleotide adenylyltransferase
B: Nicotinamide-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,43912
Polymers74,0942
Non-polymers1,34510
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-0 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.988, 60.536, 202.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 37 through 75 or resid 77 through 701))
d_2ens_1(chain "B" and (resid 37 through 75 or resid 77 through 701))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPARGARGAA37 - 7545 - 83
d_12PHEPHEGLNGLNAA77 - 28185 - 289
d_13NMNNMNNMNNMNAC401
d_14GOLGOLGOLGOLAD402
d_15PEGPEGPEGPEGAE403
d_16EDOEDOEDOEDOAF404
d_21ASPASPARGARGBB37 - 7545 - 83
d_22PHEPHEGLNGLNBB77 - 28185 - 289
d_23NMNNMNNMNNMNBI401
d_24GOLGOLGOLGOLBJ402
d_25PEGPEGPEGPEGBK403
d_26EDOEDOEDOEDOBL404

NCS oper: (Code: givenMatrix: (0.233451245087, -0.579018331614, 0.781177500842), (-0.578072935227, -0.728634812031, -0.3673186522), (0.781877354657, -0.365826574146, -0.504815530589)Vector: -23. ...NCS oper: (Code: given
Matrix: (0.233451245087, -0.579018331614, 0.781177500842), (-0.578072935227, -0.728634812031, -0.3673186522), (0.781877354657, -0.365826574146, -0.504815530589)
Vector: -23.0843696455, 12.4270114911, 46.1342095798)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nicotinamide-nucleotide adenylyltransferase / NMN/NaMN adenylyltransferase


Mass: 37046.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0044330 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G0S929, nicotinamide-nucleotide adenylyltransferase, nicotinate-nucleotide adenylyltransferase

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Non-polymers , 5 types, 297 molecules

#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.77 Å3/Da / Density % sol: 30.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 22% PEG3350; 0.1M sodium nitrate; 0.01 M spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 31285 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 23.16 Å2 / CC1/2: 0.985 / Net I/σ(I): 12.3
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1533 / CC1/2: 0.811 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→45.03 Å / SU ML: 0.1853 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 1385 4.77 %
Rwork0.1924 27626 -
obs0.1943 29011 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.55 Å2
Refinement stepCycle: LAST / Resolution: 2.11→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 88 287 4285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624095
X-RAY DIFFRACTIONf_angle_d0.93965548
X-RAY DIFFRACTIONf_chiral_restr0.0591610
X-RAY DIFFRACTIONf_plane_restr0.0078711
X-RAY DIFFRACTIONf_dihedral_angle_d6.8447564
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.25248381158 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.180.2809810.22871546X-RAY DIFFRACTION52.84
2.18-2.270.26351300.22062271X-RAY DIFFRACTION77.75
2.27-2.380.28051530.22272852X-RAY DIFFRACTION97.53
2.38-2.50.26731330.21452932X-RAY DIFFRACTION99.29
2.5-2.660.2821360.21142947X-RAY DIFFRACTION99.04
2.66-2.860.25421310.21492976X-RAY DIFFRACTION99.11
2.86-3.150.25321430.20142934X-RAY DIFFRACTION99.32
3.15-3.610.21241580.18242988X-RAY DIFFRACTION99.59
3.61-4.540.19811490.15852995X-RAY DIFFRACTION98.56
4.54-45.030.20231710.18463185X-RAY DIFFRACTION99.53

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