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- PDB-9yeb: Nickel Pincer Mononucleotide-Dependent NphT -

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Basic information

Entry
Database: PDB / ID: 9yeb
TitleNickel Pincer Mononucleotide-Dependent NphT
ComponentsOxidoreductase
KeywordsBIOSYNTHETIC PROTEIN / Nickel pincer mononucleotide-dependent hydride transferase
Function / homology: / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / oxidoreductase activity / Chem-4EY / NICKEL (II) ION / Oxidoreductase
Function and homology information
Biological speciesPaenalicyclobacillus cellulosilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsNeugebauer, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
David and Lucile Packard Foundation United States
CitationJournal: To Be Published
Title: Nickel Pincer Mononucleotide-Dependent NphT
Authors: Neugebauer, M.E.
History
DepositionSep 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1668
Polymers65,2102
Non-polymers9566
Water16,069892
1
A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0834
Polymers32,6051
Non-polymers4783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0834
Polymers32,6051
Non-polymers4783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.597, 49.151, 79.218
Angle α, β, γ (deg.)90.00, 117.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oxidoreductase


Mass: 32605.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenalicyclobacillus cellulosilyticus (bacteria)
Gene: GCM10010885_09220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A917NHY8
#2: Chemical ChemComp-4EY / 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium / Dithiodinicotinic acid mononucleotide


Mass: 396.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO8PS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium Acetate pH 4.5, 200 mM ammonium chloride, 25.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 194 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 1.3→70.37 Å / Num. obs: 246252 / % possible obs: 99.15 % / Redundancy: 2 % / Biso Wilson estimate: 9.58 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.62
Reflection shellResolution: 1.3→1.31 Å / Mean I/σ(I) obs: 1.72 / Num. unique obs: 4003 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→70.37 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 6233 5.06 %
Rwork0.1448 --
obs0.1459 123212 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→70.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 52 892 5504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095140
X-RAY DIFFRACTIONf_angle_d1.1527002
X-RAY DIFFRACTIONf_dihedral_angle_d15.0441983
X-RAY DIFFRACTIONf_chiral_restr0.083740
X-RAY DIFFRACTIONf_plane_restr0.013936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.352070.38063790X-RAY DIFFRACTION98
1.31-1.330.35011820.33033841X-RAY DIFFRACTION97
1.33-1.350.26012060.27883858X-RAY DIFFRACTION99
1.35-1.360.21242120.23483815X-RAY DIFFRACTION97
1.36-1.380.20152190.19813802X-RAY DIFFRACTION99
1.38-1.40.20731920.18733865X-RAY DIFFRACTION98
1.4-1.420.2222080.17733859X-RAY DIFFRACTION99
1.42-1.440.19642220.17233872X-RAY DIFFRACTION99
1.44-1.460.19892010.1653871X-RAY DIFFRACTION99
1.46-1.490.18552190.17663856X-RAY DIFFRACTION99
1.49-1.510.20262170.17693830X-RAY DIFFRACTION99
1.51-1.540.21132220.18873866X-RAY DIFFRACTION99
1.54-1.570.18031880.14143898X-RAY DIFFRACTION100
1.57-1.60.16322090.13263903X-RAY DIFFRACTION99
1.6-1.640.172030.12973932X-RAY DIFFRACTION99
1.64-1.680.17421900.12633890X-RAY DIFFRACTION100
1.68-1.720.1421970.12633898X-RAY DIFFRACTION100
1.72-1.760.15812260.12443954X-RAY DIFFRACTION100
1.76-1.820.15521940.13173900X-RAY DIFFRACTION100
1.82-1.870.14382120.12943915X-RAY DIFFRACTION100
1.87-1.940.15512170.12963926X-RAY DIFFRACTION100
1.94-2.020.142260.12833895X-RAY DIFFRACTION100
2.02-2.110.15082040.1243939X-RAY DIFFRACTION100
2.11-2.220.15131900.12093986X-RAY DIFFRACTION100
2.22-2.360.1572120.12193914X-RAY DIFFRACTION100
2.36-2.540.14692270.12893915X-RAY DIFFRACTION100
2.54-2.80.15631950.12953976X-RAY DIFFRACTION100
2.8-3.210.17222300.13143957X-RAY DIFFRACTION100
3.21-4.040.142210.12523981X-RAY DIFFRACTION100
4.04-70.370.15371850.15424075X-RAY DIFFRACTION99

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