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- PDB-9kyf: Crystal structure of E.coli ac4C amidohydrolase YqfB -

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Basic information

Entry
Database: PDB / ID: 9kyf
TitleCrystal structure of E.coli ac4C amidohydrolase YqfB
ComponentsN(4)-acetylcytidine amidohydrolase
KeywordsHYDROLASE / N4-acetylcytidine / RNA modification / amidohydrolase
Function / homology:
Function and homology information
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGuo, W.T. / Wu, B.X. / Meng, C.Y. / Wen, Y.
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)23,8453
Polymers23,8052
Non-polymers401
Water6,269348
1
A: N(4)-acetylcytidine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9422
Polymers11,9021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N(4)-acetylcytidine amidohydrolase


Theoretical massNumber of molelcules
Total (without water)11,9021
Polymers11,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.306, 30.550, 61.949
Angle α, β, γ (deg.)90.000, 93.897, 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
11B-234-

HOH

21B-326-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 27 or (resid 28...
d_2ens_1(chain "B" and (resid 3 through 78 or resid 80 through 103))

NCS domain segments:

Ens-ID: ens_1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROAA3 - 783 - 78
d_12GLUGLUAA80 - 10380 - 103
d_21PROPROBB3 - 783 - 78
d_22GLUGLUBB80 - 10380 - 103

NCS oper: (Code: givenMatrix: (0.550853893828, 0.0087038533687, 0.834556307621), (0.000876668417299, -0.999951101724, 0.00985015807674), (0.834601233588, -0.00469436877405, -0.550834588416)Vector: - ...NCS oper: (Code: given
Matrix: (0.550853893828, 0.0087038533687, 0.834556307621), (0.000876668417299, -0.999951101724, 0.00985015807674), (0.834601233588, -0.00469436877405, -0.550834588416)
Vector: -12.6552110156, 20.3646539699, -3.35665783229)

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium acetate, 0.1 M MES pH 6.0, 20% w/v Polyethylene glycol 8,000

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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: 1.55→30 Å / Num. obs: 29807 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.24 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Net I/σ(I): 13.4
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 6 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 4293 / CC1/2: 0.979 / Rpim(I) all: 0.08 / Rrim(I) all: 0.197 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.4 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.8406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 1510 5.07 %
Rwork0.2013 28288 -
obs0.2035 29798 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.84 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 1 348 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581667
X-RAY DIFFRACTIONf_angle_d0.80882259
X-RAY DIFFRACTIONf_chiral_restr0.0582267
X-RAY DIFFRACTIONf_plane_restr0.0069292
X-RAY DIFFRACTIONf_dihedral_angle_d16.0888608
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.810683167265 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.2721070.22882574X-RAY DIFFRACTION99.85
1.6-1.660.30511270.23282538X-RAY DIFFRACTION99.93
1.66-1.720.28411540.24482536X-RAY DIFFRACTION99.96
1.72-1.80.26931550.2342539X-RAY DIFFRACTION99.96
1.8-1.90.30181380.22572548X-RAY DIFFRACTION99.89
1.9-2.020.26251410.21222559X-RAY DIFFRACTION99.96
2.02-2.170.24711430.20692560X-RAY DIFFRACTION99.7
2.17-2.390.25691430.19952555X-RAY DIFFRACTION99.93
2.39-2.740.2211470.20942568X-RAY DIFFRACTION99.74
2.74-3.450.23961280.19312616X-RAY DIFFRACTION99.78
3.45-29.40.21711270.17582695X-RAY DIFFRACTION99.61

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