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- PDB-8x6w: Crystal structure of EfCDA -

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Basic information

Entry
Database: PDB / ID: 8x6w
TitleCrystal structure of EfCDA
ComponentsEfCDA
KeywordsHYDROLASE / cytidine deaminase
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)29,1084
Polymers28,9772
Non-polymers1312
Water5,603311
1
A: EfCDA
B: EfCDA
hetero molecules

A: EfCDA
B: EfCDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2158
Polymers57,9544
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area10700 Å2
ΔGint-226 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.331, 83.331, 81.702
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
11B-411-

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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 56.12 %
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 PILATUS 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: 30010 / % possible obs: 89.4 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 25.5
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.327 / Num. unique obs: 1679

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.75→29.17 Å / SU ML: 0.1546 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.4349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 1996 6.68 %
Rwork0.1832 27873 -
obs0.1849 29869 88.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 2 311 2321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932054
X-RAY DIFFRACTIONf_angle_d1.09872798
X-RAY DIFFRACTIONf_chiral_restr0.0617320
X-RAY DIFFRACTIONf_plane_restr0.009366
X-RAY DIFFRACTIONf_dihedral_angle_d5.3122280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.24781580.17942166X-RAY DIFFRACTION97.89
1.79-1.840.22381580.17012191X-RAY DIFFRACTION99.11
1.84-1.90.18121530.17352201X-RAY DIFFRACTION98.87
1.9-1.960.19351530.1682136X-RAY DIFFRACTION97.86
1.96-2.030.20061590.1752154X-RAY DIFFRACTION97.23
2.03-2.110.18511470.18192090X-RAY DIFFRACTION94.71
2.11-2.20.21521510.18592077X-RAY DIFFRACTION92.76
2.2-2.320.22931390.17651989X-RAY DIFFRACTION89.3
2.32-2.470.18851350.1881934X-RAY DIFFRACTION87.52
2.47-2.660.1891400.19531914X-RAY DIFFRACTION85.19
2.66-2.920.23611340.20641849X-RAY DIFFRACTION82.9
2.92-3.340.24341200.19581761X-RAY DIFFRACTION77.73
3.34-4.210.18281200.16831663X-RAY DIFFRACTION73.22
4.21-29.170.21461290.18471748X-RAY DIFFRACTION73.64

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