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- PDB-7ww2: Structure of an Isocytosine specific deaminase Vcz -

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Basic information

Entry
Database: PDB / ID: 7ww2
TitleStructure of an Isocytosine specific deaminase Vcz
Components8-oxoguanine deaminase
KeywordsHYDROLASE / deaminase / isocytosine / cancer therapy / 5-fluorouracil
Function / homology8-oxoguanine deaminase activity / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / Hydroxydechloroatrazine ethylaminohydrolase
Function and homology information
Biological speciesObesumbacterium proteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLi, 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
DepositionFeb 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 8-oxoguanine deaminase
B: 8-oxoguanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2204
Polymers99,0892
Non-polymers1312
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-108 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.442, 107.523, 120.506
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 29 through 208 or resid 210 through 476))
d_2ens_1(chain "B" and (resid 29 through 208 or resid 210 through 476))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGASPASPAA29 - 2084 - 183
d_12LEULEUASNASNAA210 - 476185 - 451
d_21ARGARGASPASPBB29 - 2084 - 183
d_22LEULEUASNASNBB210 - 476185 - 451

NCS oper: (Code: givenMatrix: (-0.994547817682, -0.103989117524, -0.00780395933365), (-0.10421398802, 0.988423534813, 0.110264956034), (-0.00375273840167, 0.110477053115, -0.993871590141)Vector: -5. ...NCS oper: (Code: given
Matrix: (-0.994547817682, -0.103989117524, -0.00780395933365), (-0.10421398802, 0.988423534813, 0.110264956034), (-0.00375273840167, 0.110477053115, -0.993871590141)
Vector: -5.69131646847, 2.73685310674, -54.8797471108)

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Components

#1: Protein 8-oxoguanine deaminase / 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, EYY98_15020 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Q9D6T1, EC: 3.5.4.32
#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.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium malonate pH 7.0, 20% 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: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 25076 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 28.57 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Net I/σ(I): 18.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 3613 / CC1/2: 0.963 / Rpim(I) all: 0.214 / Rrim(I) all: 0.576 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.76 Å / SU ML: 0.2989 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2417 1247 5.01 %
Rwork0.182 23631 -
obs0.185 24878 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.27 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6820 0 2 91 6913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826948
X-RAY DIFFRACTIONf_angle_d1.12719424
X-RAY DIFFRACTIONf_chiral_restr0.05681072
X-RAY DIFFRACTIONf_plane_restr0.01091250
X-RAY DIFFRACTIONf_dihedral_angle_d7.511975
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.71006930743 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.31641370.22082604X-RAY DIFFRACTION99.96
2.81-2.940.29561410.20292601X-RAY DIFFRACTION99.96
2.94-3.090.25221390.20262613X-RAY DIFFRACTION99.93
3.09-3.280.2821510.21562587X-RAY DIFFRACTION99.96
3.28-3.540.33651380.22382533X-RAY DIFFRACTION97.13
3.54-3.890.24121260.19842600X-RAY DIFFRACTION98.06
3.89-4.450.22371400.15952621X-RAY DIFFRACTION98.75
4.45-5.60.1691350.1412680X-RAY DIFFRACTION99.96
5.61-29.760.17151400.14122792X-RAY DIFFRACTION99.09
Refinement TLS params.Method: refined / Origin x: -1.96421506634 Å / Origin y: -15.8795070429 Å / Origin z: -28.2430535083 Å
111213212223313233
T0.144973916491 Å20.023395423809 Å2-0.00212248558242 Å2-0.0937109146012 Å2-0.0102298304388 Å2--0.162197178798 Å2
L1.90021139392 °2-0.0587248438425 °20.657808949959 °2-0.536066874345 °2-0.0524344509973 °2--0.980841174385 °2
S-0.108332525711 Å °-0.0630985807051 Å °0.206532611254 Å °-0.023305415103 Å °0.0137423682806 Å °-0.0449854713671 Å °-0.104227904024 Å °-0.0182718398445 Å °0.0669505082364 Å °
Refinement TLS groupSelection details: all

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