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- PDB-9kyh: Crystal structure of E.coli ac4C amidohydrolase YqfB in complex w... -

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Basic information

Entry
Database: PDB / ID: 9kyh
TitleCrystal structure of E.coli ac4C amidohydrolase YqfB in complex with ac4C
ComponentsN(4)-acetylcytidine amidohydrolase
KeywordsHYDROLASE / N4-acetylcytidine / RNA modification / amidohydrolase / cytidine / complex
Function / homology: / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / :
Function and homology information
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsGuo, W.T. / Meng, C.Y. / Wen, Y. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing.
Authors: Meng, C. / Shi, X. / Guo, W. / Jian, X. / Zhao, J. / Wen, Y. / Wang, R. / Li, Y. / Xu, S. / Chen, H. / Zhang, J. / Chen, M. / Chen, H. / Wu, B.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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: N(4)-acetylcytidine amidohydrolase
B: N(4)-acetylcytidine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3575
Polymers23,8052
Non-polymers5533
Water6,684371
1
A: N(4)-acetylcytidine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1703
Polymers11,9021
Non-polymers2682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint3 kcal/mol
Surface area5450 Å2
MethodPISA
2
B: N(4)-acetylcytidine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1882
Polymers11,9021
Non-polymers2851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-3 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.570, 30.480, 61.610
Angle α, β, γ (deg.)90.000, 94.190, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

21B-301-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 3 through 103)
d_2ens_1(chain "B" and (resid 3 through 98 or (resid 99...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 3 - 103 / Label seq-ID: 3 - 103

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.556734422974, 0.0168280549833, 0.830520077326), (0.00690245832418, -0.99985398631, 0.0156320865192), (0.830661867636, -0.00297029044699, -0.556769287074)Vector: -12. ...NCS oper: (Code: given
Matrix: (0.556734422974, 0.0168280549833, 0.830520077326), (0.00690245832418, -0.99985398631, 0.0156320865192), (0.830661867636, -0.00297029044699, -0.556769287074)
Vector: -12.2258854915, 20.5002837626, -3.18070105754)

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Components

#1: Protein N(4)-acetylcytidine amidohydrolase / ac4C amidohydrolase


Mass: 11902.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ECBD_0837 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A140N8S3, N4-acetylcytidine amidohydrolase
#2: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1EHT / N4-Acetylcytidine


Mass: 285.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N3O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. obs: 30235 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 15.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.046 / Rrim(I) all: 0.112 / Net I/σ(I): 10.1
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2 / Num. unique obs: 4360 / CC1/2: 0.728 / Rpim(I) all: 0.372 / Rrim(I) all: 0.874 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→27.6 Å / SU ML: 0.1644 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 1490 4.93 %
Rwork0.1827 28729 -
obs0.1844 30219 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.54→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 38 371 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671710
X-RAY DIFFRACTIONf_angle_d0.90382318
X-RAY DIFFRACTIONf_chiral_restr0.0608274
X-RAY DIFFRACTIONf_plane_restr0.0077294
X-RAY DIFFRACTIONf_dihedral_angle_d7.9742229
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.795111387495 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.28531340.24372566X-RAY DIFFRACTION99.59
1.59-1.650.29191220.24352621X-RAY DIFFRACTION99.93
1.65-1.710.3151240.25452588X-RAY DIFFRACTION99.93
1.71-1.790.2711170.22522608X-RAY DIFFRACTION99.93
1.79-1.880.2211320.19412589X-RAY DIFFRACTION99.93
1.88-20.23871260.19632609X-RAY DIFFRACTION99.93
2-2.160.21561560.17412600X-RAY DIFFRACTION100
2.16-2.370.21791500.1722593X-RAY DIFFRACTION99.96
2.37-2.720.22671660.18752587X-RAY DIFFRACTION99.93
2.72-3.420.21041370.16732640X-RAY DIFFRACTION99.93
3.42-27.60.17161260.16012728X-RAY DIFFRACTION99.27

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