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- PDB-8x6y: Crystal structure of EfCDA -

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Basic information

Entry
Database: PDB / ID: 8x6y
TitleCrystal structure of EfCDA
ComponentsEfCDA
KeywordsHYDROLASE / cytidine deaminase
Function / homologyCACODYLATE ION
Function and homology information
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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

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Assembly

Deposited unit
A: EfCDA
B: EfCDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3826
Polymers28,9772
Non-polymers4054
Water6,756375
1
A: EfCDA
B: EfCDA
hetero molecules

A: EfCDA
B: EfCDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,76312
Polymers57,9544
Non-polymers8108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area10760 Å2
ΔGint-194 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.349, 55.749, 82.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 8 through 129)
d_2ens_1(chain "B" and resid 8 through 129)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 8 - 129 / Label seq-ID: 10 - 131

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.9999908748, -0.00425411222954, -0.000390955613268), (0.00295133909206, -0.754110077158, 0.656741411155), (-0.00308867523653, 0.656734264416, 0.75411575108)Vector: - ...NCS oper: (Code: given
Matrix: (-0.9999908748, -0.00425411222954, -0.000390955613268), (0.00295133909206, -0.754110077158, 0.656741411155), (-0.00308867523653, 0.656734264416, 0.75411575108)
Vector: -15.3208250053, 0.0895196151087, 0.0389550882667)

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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-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium cacodylate, pH 6.5, 20% PEG 4000

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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: 1.56→30 Å / Num. obs: 36093 / % possible obs: 99.1 % / Redundancy: 12.4 % / Biso Wilson estimate: 5.95 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 43.4
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 0.194 / Num. unique obs: 1738

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.56→28.25 Å / SU ML: 0.1207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.0156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.174 2004 5.55 %
Rwork0.1519 34089 -
obs0.1532 36093 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.62 Å2
Refinement stepCycle: LAST / Resolution: 1.56→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 12 375 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791950
X-RAY DIFFRACTIONf_angle_d1.08832662
X-RAY DIFFRACTIONf_chiral_restr0.108306
X-RAY DIFFRACTIONf_plane_restr0.0086346
X-RAY DIFFRACTIONf_dihedral_angle_d5.0711266
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.652317965834 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.18871330.15812328X-RAY DIFFRACTION95.72
1.6-1.640.15811360.14562380X-RAY DIFFRACTION98.63
1.64-1.690.17421490.14132384X-RAY DIFFRACTION98.71
1.69-1.740.16851380.14132399X-RAY DIFFRACTION98.79
1.74-1.80.17431430.14352379X-RAY DIFFRACTION98.67
1.8-1.880.16691370.1422410X-RAY DIFFRACTION98.76
1.88-1.960.16771400.1462424X-RAY DIFFRACTION99.3
1.96-2.060.18251440.15282432X-RAY DIFFRACTION99.5
2.07-2.190.17921420.14582426X-RAY DIFFRACTION99.23
2.19-2.360.16341440.15722459X-RAY DIFFRACTION99.54
2.36-2.60.18771440.15422450X-RAY DIFFRACTION99.77
2.6-2.980.17251470.16152485X-RAY DIFFRACTION99.92
2.98-3.750.15971490.14792509X-RAY DIFFRACTION99.92
3.75-28.250.18651580.16362624X-RAY DIFFRACTION99.61

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