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- PDB-1tiy: X-RAY STRUCTURE OF GUANINE DEAMINASE FROM BACILLUS SUBTILIS NORTH... -

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Basic information

Entry
Database: PDB / ID: 1tiy
TitleX-RAY STRUCTURE OF GUANINE DEAMINASE FROM BACILLUS SUBTILIS NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR160
ComponentsGuanine deaminase
KeywordsHYDROLASE / protein-Zn complex / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


guanine deaminase / guanine deaminase activity / guanine catabolic process / 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
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKuzin, A.P. / Vorobiev, S. / Edstrom, W. / Forouhar, F. / Acton, T. / Shastry, R. / Ma, L.-C. / Chiang, Y.-W. / Montelione, G. / Tong, L. ...Kuzin, A.P. / Vorobiev, S. / Edstrom, W. / Forouhar, F. / Acton, T. / Shastry, R. / Ma, L.-C. / Chiang, Y.-W. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: X-RAY STRUCTURE OF GUANINE DEAMINASE FROM BACILLUS SUBTILIS NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR160
Authors: Kuzin, A.P. / Vorobiev, S. / Edstrom, W. / Forouhar, F. / Acton, T. / Shastry, R. / Ma, L.-C. / Chiang, Y.-W. / Montelione, G. / Tong, L. / Hunt, J.F.
History
DepositionJun 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8094
Polymers36,6792
Non-polymers1312
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Guanine deaminase
hetero molecules

A: Guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8094
Polymers36,6792
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area8080 Å2
ΔGint-153 kcal/mol
Surface area13190 Å2
MethodPISA, PQS
3
B: Guanine deaminase
hetero molecules

B: Guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8094
Polymers36,6792
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
MethodPQS
Unit cell
Length a, b, c (Å)99.287, 99.287, 72.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Guanine deaminase / Guanase / Guanine aminase / Guanine aminohydrolase / GAH / GDEase


Mass: 18339.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: GUAD, GDE, BSU13170 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O34598, guanine deaminase
#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.: 64 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 1.7-1.8 M (Nh4)2So4, 0.2M K-Na Tartrate, 0.02M Na3-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914, 0.97933, 0.97778
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979141
20.979331
30.977781
ReflectionResolution: 2.5→30 Å / Num. obs: 10341 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 18.6 % / Biso Wilson estimate: 34.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.429

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.39 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 292315.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 481 4.8 %RANDOM
Rwork0.222 ---
obs0.222 9944 92.2 %-
all-10317 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.7732 Å2 / ksol: 0.321941 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.761 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 2 64 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.3911.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc-scbond_it1.9772
X-RAY DIFFRACTIONc_scangle_it3.0932.5
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.377 0
Rfree-0
obs-174
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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