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- PDB-9us2: Crystal structure of YgdH from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 9us2
TitleCrystal structure of YgdH from Neisseria meningitidis
ComponentsCytokinin riboside 5'-monophosphate phosphoribohydrolase
KeywordsHYDROLASE / Cytokinin riboside 5'-monophosphate phosphoribohydrolase with a strong preference for UMP
Function / homology
Function and homology information


: / AMP nucleosidase activity / cytokinin biosynthetic process / cytosol
Similarity search - Function
: / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase
Similarity search - Domain/homology
CITRIC ACID / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, W.Q. / Yu, L. / Chen, R.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170026 China
National Natural Science Foundation of China (NSFC)32470047 China
CitationJournal: Nat Commun / Year: 2025
Title: A combined pseudouridine biomanufacturing platform enabled by a streamlined designer pathway.
Authors: Yu, L. / Chen, R. / Zhang, C. / Wang, Z. / Wang, Z. / Zeng, X. / Liang, H. / He, Y. / She, Y. / Wang, Y. / Gong, R. / Song, X. / Deng, Z. / Fei, Q. / Chen, W.
History
DepositionMay 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3304
Polymers68,1383
Non-polymers1921
Water4,035224
1
A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules

C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase


Theoretical massNumber of molelcules
Total (without water)91,0435
Polymers90,8514
Non-polymers1921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Unit cell
Length a, b, c (Å)86.814, 142.236, 119.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cytokinin riboside 5'-monophosphate phosphoribohydrolase


Mass: 22712.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: ygdH, CNQ34_05655, COI09_06730, DE8555_0277, ERS514591_00967, ERS514851_00315
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0Y5MUU2, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20%(w/v) PEG 6000, 1 M lithium chloride, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2023
RadiationMonochromator: Sli111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→62.96 Å / Num. obs: 68487 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 27.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Rrim(I) all: 0.096 / Χ2: 0.89 / Net I/σ(I): 18.9
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.059 / Num. unique obs: 9039 / CC1/2: 0.894 / Rpim(I) all: 0.298 / Rrim(I) all: 0.026 / Χ2: 0.76

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
Aimless0.7.7data scaling
PHENIX1.19.2_4158phasing
PDB_EXTRACT4.2data extraction
HKL-30007.21data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.98 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 3424 5 %
Rwork0.2069 --
obs0.208 68487 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 13 224 4895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074774
X-RAY DIFFRACTIONf_angle_d0.856476
X-RAY DIFFRACTIONf_dihedral_angle_d5.459669
X-RAY DIFFRACTIONf_chiral_restr0.054707
X-RAY DIFFRACTIONf_plane_restr0.009859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.34411580.31142645X-RAY DIFFRACTION100
1.83-1.850.33061580.2912680X-RAY DIFFRACTION100
1.85-1.880.35541350.2772687X-RAY DIFFRACTION100
1.88-1.910.31591460.25982666X-RAY DIFFRACTION100
1.91-1.950.30011150.25092718X-RAY DIFFRACTION100
1.95-1.980.27031490.23392678X-RAY DIFFRACTION100
1.98-2.020.24091290.23692716X-RAY DIFFRACTION100
2.02-2.060.25051400.2262671X-RAY DIFFRACTION100
2.06-2.110.27881210.23532706X-RAY DIFFRACTION100
2.11-2.150.26391500.23892697X-RAY DIFFRACTION100
2.15-2.210.2161400.22612686X-RAY DIFFRACTION100
2.21-2.270.28191650.21592692X-RAY DIFFRACTION100
2.27-2.330.24551620.22942664X-RAY DIFFRACTION100
2.33-2.410.26751230.22542728X-RAY DIFFRACTION100
2.41-2.50.24261190.22992710X-RAY DIFFRACTION100
2.5-2.60.29121530.22852722X-RAY DIFFRACTION100
2.6-2.710.26651580.23782673X-RAY DIFFRACTION100
2.71-2.860.25161320.23762739X-RAY DIFFRACTION100
2.86-3.030.24561510.22722689X-RAY DIFFRACTION100
3.03-3.270.22331370.2232736X-RAY DIFFRACTION100
3.27-3.60.21621280.20022766X-RAY DIFFRACTION100
3.6-4.120.17211640.17222733X-RAY DIFFRACTION100
4.12-5.180.16171270.14762800X-RAY DIFFRACTION100
5.18-24.980.19831640.16492861X-RAY DIFFRACTION100

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