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- PDB-4lc5: Structural basis of substrate specificity of CDA superfamily guan... -

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Basic information

Entry
Database: PDB / ID: 4lc5
TitleStructural basis of substrate specificity of CDA superfamily guanine deaminase
ComponentsCytidine and deoxycytidylate deaminase zinc-binding region
KeywordsHYDROLASE / CDA fold / deaminase
Function / homology
Function and homology information


guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
9-METHYLGUANINE / Cytidine and deoxycytidylate deaminase zinc-binding region
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBitra, A. / Biswas, A. / Anand, R.
CitationJournal: Biochemistry / Year: 2013
Title: Structural basis of the substrate specificity of cytidine deaminase superfamily Guanine deaminase
Authors: Bitra, A. / Biswas, A. / Anand, R.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytidine and deoxycytidylate deaminase zinc-binding region
B: Cytidine and deoxycytidylate deaminase zinc-binding region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6558
Polymers41,1732
Non-polymers4826
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-91 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.150, 74.180, 109.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytidine and deoxycytidylate deaminase zinc-binding region


Mass: 20586.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / NBRC 14298 / Production host: Escherichia coli (E. coli)
References: UniProt: Q82Y41, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9MG / 9-METHYLGUANINE


Mass: 165.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.225M MgCl2, 25% PEG 3350, 0.1M Bis-Tris (pH- 5.5), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.97→38.15 Å / Num. all: 21731 / Num. obs: 21731 / % possible obs: 94.8 % / Redundancy: 3.7 % / Rsym value: 0.059 / Net I/σ(I): 13
Reflection shellResolution: 1.97→2.07 Å / % possible obs: 87.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 5.9 / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→37.09 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.34 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1994 9.2 %RANDOM
Rwork0.1645 ---
obs0.1692 21692 94.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.1 Å2 / Biso mean: 22.1854 Å2 / Biso min: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.97→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 26 145 2884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192793
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9773802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98123.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42115412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0531525
X-RAY DIFFRACTIONr_chiral_restr0.1380.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212153
LS refinement shellResolution: 1.965→2.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 111 -
Rwork0.159 1203 -
all-1314 -
obs--84.5 %

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