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- PDB-8x6u: Crystal structure of EfCDA in complex with dFdU -

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Basic information

Entry
Database: PDB / ID: 8x6u
TitleCrystal structure of EfCDA in complex with dFdU
ComponentsEfCDA
KeywordsHYDROLASE / cytidine deaminase / gemcitabine / dFdU
Function / homology:
Function and homology information
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJiang, L. / Huang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
National Natural Science Foundation of China (NSFC)31870741 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Deciphering the role of Enterococcus faecium cytidine deaminase in gemcitabine resistance of gallbladder cancer.
Authors: Jiang, L. / Zhang, L. / Shu, Y. / Zhang, Y. / Gao, L. / Qiu, S. / Zhang, W. / Dai, W. / Chen, S. / Huang, Y. / Liu, Y.
History
DepositionNov 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 11, 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.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

Downloads & links

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Assembly

Deposited unit
A: EfCDA
B: EfCDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6366
Polymers28,9772
Non-polymers6594
Water5,819323
1
A: EfCDA
B: EfCDA
hetero molecules

A: EfCDA
B: EfCDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,27212
Polymers57,9544
Non-polymers1,3188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area10620 Å2
ΔGint-84 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.914, 82.914, 81.646
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21B-414-

HOH

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Components

#1: Protein EfCDA


Mass: 14488.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WP_002291109.1 / Source: (gene. exp.) Enterococcus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-Y7U / 2',2'-Difluorodeoxyuridine / 1-[(2~{R},4~{R},5~{R})-3,3-bis(fluoranyl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidine-2,4-dione


Mass: 264.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10F2N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.5, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 33271 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 19.92 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 48.5
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.439 / Num. unique obs: 1637

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.75→29.09 Å / SU ML: 0.1335 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.9009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1857 2001 6.01 %
Rwork0.1612 31270 -
obs0.1627 33271 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 38 323 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732092
X-RAY DIFFRACTIONf_angle_d0.97862856
X-RAY DIFFRACTIONf_chiral_restr0.0587328
X-RAY DIFFRACTIONf_plane_restr0.0087368
X-RAY DIFFRACTIONf_dihedral_angle_d8.1082306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.23451410.19222170X-RAY DIFFRACTION97.92
1.79-1.840.23241390.17442197X-RAY DIFFRACTION100
1.84-1.890.2171370.18432195X-RAY DIFFRACTION100
1.89-1.950.20921410.17852219X-RAY DIFFRACTION100
1.95-2.020.22151420.17942216X-RAY DIFFRACTION100
2.02-2.110.18881440.1632223X-RAY DIFFRACTION100
2.11-2.20.17251400.17572226X-RAY DIFFRACTION100
2.2-2.320.19381430.172232X-RAY DIFFRACTION100
2.32-2.460.18141420.17412205X-RAY DIFFRACTION100
2.46-2.650.21481400.16392251X-RAY DIFFRACTION100
2.65-2.920.20931460.17082228X-RAY DIFFRACTION100
2.92-3.340.19261480.16522256X-RAY DIFFRACTION100
3.34-4.20.12521450.13912278X-RAY DIFFRACTION100
4.21-29.090.1861530.14352374X-RAY DIFFRACTION99.8

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