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- PDB-8is4: Structure of an Isocytosine specific deaminase Vcz in complexed w... -

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Basic information

Entry
Database: PDB / ID: 8is4
TitleStructure of an Isocytosine specific deaminase Vcz in complexed with 5-FU
ComponentsHydroxydechloroatrazine ethylaminohydrolase
KeywordsHYDROLASE / isocytosine / deaminase / VCZ / 5-FU
Function / homology8-oxoguanine deaminase activity / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / 5-FLUOROURACIL / Hydroxydechloroatrazine ethylaminohydrolase
Function and homology information
Biological speciesObesumbacterium proteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuo, W.T. / Li, X.J. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iscience / Year: 2023
Title: Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy.
Authors: Guo, W. / Li, X. / Fan, J. / Li, H. / Wen, Y. / Meng, C. / Chen, H. / Zhao, Z. / Zhang, Y. / Du, Y. / Wu, B.
History
DepositionMar 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxydechloroatrazine ethylaminohydrolase
B: Hydroxydechloroatrazine ethylaminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6948
Polymers99,0892
Non-polymers6056
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-104 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.388, 107.986, 120.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 106 or resid 108...
d_2ens_1(chain "B" and (resid 3 through 106 or resid 108...

NCS oper: (Code: givenMatrix: (-0.993624241163, -0.112149118858, -0.0115517319768), (-0.112718522023, 0.986072437462, 0.122293429385), (-0.00232425584038, 0.122815810127, -0.992426760329)Vector: -5. ...NCS oper: (Code: given
Matrix: (-0.993624241163, -0.112149118858, -0.0115517319768), (-0.112718522023, 0.986072437462, 0.122293429385), (-0.00232425584038, 0.122815810127, -0.992426760329)
Vector: -5.29903880537, 3.0679142214, -54.8724390171)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hydroxydechloroatrazine ethylaminohydrolase


Mass: 49544.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obesumbacterium proteus (bacteria) / Gene: DSM2777_13610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Q9D6T1

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Non-polymers , 5 types, 576 molecules

#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Bis-Tris, pH 6.5, 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: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 71085 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.041 / Rrim(I) all: 0.15 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10243 / CC1/2: 0.822 / Rpim(I) all: 0.298 / Rrim(I) all: 1.086 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.67 Å / SU ML: 0.1631 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1888 3563 5.02 %
Rwork0.1546 67426 -
obs0.1564 70989 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6814 0 34 570 7418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00777030
X-RAY DIFFRACTIONf_angle_d1.00679542
X-RAY DIFFRACTIONf_chiral_restr0.06091080
X-RAY DIFFRACTIONf_plane_restr0.01611266
X-RAY DIFFRACTIONf_dihedral_angle_d6.2786994
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.667062415366 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.2371390.20372635X-RAY DIFFRACTION100
1.93-1.950.25321410.19282677X-RAY DIFFRACTION99.96
1.95-1.980.22991410.19252644X-RAY DIFFRACTION99.96
1.98-2.010.19741320.18692679X-RAY DIFFRACTION100
2.01-2.050.22121340.17722663X-RAY DIFFRACTION100
2.05-2.080.21711460.16992666X-RAY DIFFRACTION100
2.08-2.120.18731310.1672695X-RAY DIFFRACTION99.96
2.12-2.160.24741360.16222678X-RAY DIFFRACTION99.96
2.16-2.20.22011440.16112675X-RAY DIFFRACTION99.93
2.2-2.250.19751360.16172660X-RAY DIFFRACTION100
2.25-2.30.19051520.16172648X-RAY DIFFRACTION100
2.31-2.360.20091500.15942695X-RAY DIFFRACTION100
2.36-2.430.21131410.16112665X-RAY DIFFRACTION100
2.43-2.50.20171460.17032669X-RAY DIFFRACTION99.96
2.5-2.580.21631510.16412681X-RAY DIFFRACTION100
2.58-2.670.21371460.16172698X-RAY DIFFRACTION100
2.67-2.780.2061500.16732679X-RAY DIFFRACTION100
2.78-2.90.18891440.16232727X-RAY DIFFRACTION100
2.9-3.060.20971330.1672677X-RAY DIFFRACTION100
3.06-3.250.23551450.16152730X-RAY DIFFRACTION100
3.25-3.50.15721380.14952706X-RAY DIFFRACTION100
3.5-3.850.18191430.13952746X-RAY DIFFRACTION100
3.85-4.410.1491290.12272765X-RAY DIFFRACTION99.93
4.41-5.550.14281410.13052787X-RAY DIFFRACTION100
5.55-34.670.15721740.14832881X-RAY DIFFRACTION99.64
Refinement TLS params.Method: refined / Origin x: -1.81018594995 Å / Origin y: -15.6613894691 Å / Origin z: -28.3216593537 Å
111213212223313233
T0.137640106666 Å20.00318865803864 Å20.00392757117122 Å2-0.0986812254801 Å20.00283875709355 Å2--0.131328668781 Å2
L1.0426707365 °2-0.000885556504104 °20.268225180668 °2-0.457039773361 °2-0.0378665464301 °2--0.596918817819 °2
S-0.0584750599358 Å °0.0436351975196 Å °0.047533879652 Å °-0.0448069283917 Å °0.0322809554492 Å °0.00334376063641 Å °-0.0670758704122 Å °-0.00775253739887 Å °0.0257269895472 Å °
Refinement TLS groupSelection details: all

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