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- PDB-6kw6: Crystal Structure of cytidine deaminase from Streptomyces noursei -

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Basic information

Entry
Database: PDB / ID: 6kw6
TitleCrystal Structure of cytidine deaminase from Streptomyces noursei
Componentscytidine deaminase
KeywordsHYDROLASE
Biological speciesStreptomyces noursei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.895 Å
AuthorsXie, T. / Liu, Z.C. / Wang, G.G.
CitationJournal: To Be Published
Title: Crystal Structure of cytidine deaminase from Streptomyces noursei
Authors: Xie, T. / Liu, Z.C. / Wang, G.G.
History
DepositionSep 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cytidine deaminase
B: cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0914
Polymers27,9602
Non-polymers1312
Water2,774154
1
A: cytidine deaminase
B: cytidine deaminase
hetero molecules

A: cytidine deaminase
B: cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1818
Polymers55,9204
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7900 Å2
ΔGint-212 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.773, 74.259, 52.785
Angle α, β, γ (deg.)90.000, 106.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21B-313-

HOH

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Components

#1: Protein cytidine deaminase


Mass: 13979.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces noursei (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH8.5 and 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: BL17U / Wavelength: 0.97916 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.89→29.933 Å / Num. obs: 19489 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.2
Reflection shellResolution: 1.89→1.93 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 992

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mpz

3mpz


Resolution: 1.895→29.933 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.09
RfactorNum. reflection% reflection
Rfree0.1922 916 4.7 %
Rwork0.168 --
obs0.1692 19486 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.22 Å2 / Biso mean: 31.2394 Å2 / Biso min: 19.66 Å2
Refinement stepCycle: final / Resolution: 1.895→29.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 2 154 1864
Biso mean--34.75 40.97 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061740
X-RAY DIFFRACTIONf_angle_d0.8242370
X-RAY DIFFRACTIONf_chiral_restr0.054270
X-RAY DIFFRACTIONf_plane_restr0.005316
X-RAY DIFFRACTIONf_dihedral_angle_d14.2551026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8955-1.99540.24841270.2011255194
1.9954-2.12040.20971190.168266198
2.1204-2.2840.22341320.166265698
2.284-2.51380.19241140.166269298
2.5138-2.87730.19371300.18265499
2.8773-3.62410.18081410.166270399
3.6241-29.9330.18361530.1618265397

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