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- PDB-9hdm: Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H... -

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Basic information

Entry
Database: PDB / ID: 9hdm
TitleCrystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa in complex with thymidine
ComponentsClavaminate synthase-like protein
KeywordsOXIDOREDUCTASE / alpha-ketoglutarate-dependent dioxygenase / nucleoside hydroxylase
Function / homologyIsopenicillin N synthase-like superfamily / metal ion binding / (R,R)-2,3-BUTANEDIOL / : / THYMIDINE / Clavaminate synthase-like protein
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFriedrich, F. / Genz, F. / Einsle, O. / Mueller, M. / Fessner, N.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Identification and Characterization of Pyrimidine Nucleoside 2'-Hydroxylase
Authors: Genz, F. / Friedrich, F. / Lonarz, C. / Einsle, O. / Jung, M. / Muller, M. / Fessner, N.D.
History
DepositionNov 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clavaminate synthase-like protein
B: Clavaminate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7999
Polymers85,0172
Non-polymers7827
Water11,782654
1
A: Clavaminate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8684
Polymers42,5091
Non-polymers3593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Clavaminate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9315
Polymers42,5091
Non-polymers4234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.983, 108.293, 115.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Clavaminate synthase-like protein


Mass: 42508.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: NCU02560 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SHQ5

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Non-polymers , 6 types, 661 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 % (w/v) PEG 3350, 0.2 M MgCl2 x 6 H2O and 0.1 M HEPES at pH 7.5; Co-crystallized with 15 mM thymidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.55→115.73 Å / Num. obs: 106321 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Χ2: 0.95 / Net I/σ(I): 17.1 / Num. measured all: 1406879
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 2.827 / Num. measured all: 70054 / Num. unique obs: 5222 / CC1/2: 0.535 / Rpim(I) all: 0.799 / Rrim(I) all: 2.939 / Χ2: 0.88 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→40.96 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 5425 5.11 %
Rwork0.1745 --
obs0.1758 106195 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 47 654 5965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065493
X-RAY DIFFRACTIONf_angle_d0.8447484
X-RAY DIFFRACTIONf_dihedral_angle_d10.9962046
X-RAY DIFFRACTIONf_chiral_restr0.056845
X-RAY DIFFRACTIONf_plane_restr0.007983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.38811670.34043360X-RAY DIFFRACTION100
1.57-1.590.38211780.32553293X-RAY DIFFRACTION100
1.59-1.610.31441830.29813305X-RAY DIFFRACTION100
1.61-1.630.30721920.27423300X-RAY DIFFRACTION100
1.63-1.650.27761750.26523300X-RAY DIFFRACTION100
1.65-1.670.26461810.24823352X-RAY DIFFRACTION100
1.67-1.690.25481900.24163311X-RAY DIFFRACTION100
1.69-1.720.26351920.21993302X-RAY DIFFRACTION100
1.72-1.750.23761860.20563312X-RAY DIFFRACTION100
1.75-1.770.21112030.20273318X-RAY DIFFRACTION100
1.77-1.80.22911840.20593341X-RAY DIFFRACTION100
1.8-1.840.2331480.19913356X-RAY DIFFRACTION100
1.84-1.870.24121870.20783314X-RAY DIFFRACTION100
1.87-1.910.24521590.20823343X-RAY DIFFRACTION100
1.91-1.950.20261850.19383352X-RAY DIFFRACTION100
1.95-20.19861800.18653343X-RAY DIFFRACTION100
2-2.050.21511970.17913328X-RAY DIFFRACTION100
2.05-2.10.19361830.17433322X-RAY DIFFRACTION100
2.1-2.170.19742120.16743331X-RAY DIFFRACTION100
2.17-2.240.18771620.16613391X-RAY DIFFRACTION100
2.24-2.320.21531800.17333371X-RAY DIFFRACTION100
2.32-2.410.20721870.17623352X-RAY DIFFRACTION100
2.41-2.520.20061820.17733380X-RAY DIFFRACTION100
2.52-2.650.19561500.16723380X-RAY DIFFRACTION100
2.65-2.820.20131860.16853373X-RAY DIFFRACTION100
2.82-3.030.19071880.17423387X-RAY DIFFRACTION100
3.03-3.340.20311570.16653411X-RAY DIFFRACTION100
3.34-3.820.15951960.14993432X-RAY DIFFRACTION100
3.82-4.810.1621660.13413499X-RAY DIFFRACTION100
4.81-40.960.19681890.16893611X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.7004 Å / Origin y: 21.0525 Å / Origin z: -34.677 Å
111213212223313233
T0.1757 Å20.009 Å20.0129 Å2-0.1633 Å20.0191 Å2--0.1914 Å2
L0.5002 °20.2574 °20.4594 °2-0.3698 °20.2327 °2--0.7325 °2
S-0.0121 Å °0.0116 Å °-0.0183 Å °-0.0056 Å °0.0079 Å °-0.013 Å °0.0106 Å °0.0239 Å °0.0046 Å °
Refinement TLS groupSelection details: all

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