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- PDB-3cl6: Crystal structure of Puue Allantoinase -

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Basic information

Entry
Database: PDB / ID: 3cl6
TitleCrystal structure of Puue Allantoinase
ComponentsPuue allantoinase
KeywordsHYDROLASE / Allantoin / Uric acid / nitrogen fixation
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process
Similarity search - Function
PuuE allantoinase/chitin deacetylase 1 / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NodB homology domain-containing protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsRamazzina, I. / Cendron, L. / Folli, C. / Berni, R. / Monteverdi, D. / Zanotti, G. / Percudani, R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases
Authors: Ramazzina, I. / Cendron, L. / Folli, C. / Berni, R. / Monteverdi, D. / Zanotti, G. / Percudani, R.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Puue allantoinase
B: Puue allantoinase


Theoretical massNumber of molelcules
Total (without water)70,9362
Polymers70,9362
Non-polymers00
Water5,260292
1
A: Puue allantoinase

A: Puue allantoinase

A: Puue allantoinase

A: Puue allantoinase


Theoretical massNumber of molelcules
Total (without water)141,8724
Polymers141,8724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area15180 Å2
ΔGint-28 kcal/mol
Surface area40590 Å2
MethodPISA
2
B: Puue allantoinase

B: Puue allantoinase

B: Puue allantoinase

B: Puue allantoinase


Theoretical massNumber of molelcules
Total (without water)141,8724
Polymers141,8724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15260 Å2
ΔGint-12 kcal/mol
Surface area39330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.299, 98.299, 62.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21B-329-

HOH

31B-330-

HOH

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Components

#1: Protein Puue allantoinase


Mass: 35468.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pGEM-Puue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q3KFK7*PLUS, allantoinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE HAS BEEN DEPOSITED IN GENEBANK, WITH ACCESSION CODE EU293536, AND IT WILL BE LOCATED ...THIS SEQUENCE HAS BEEN DEPOSITED IN GENEBANK, WITH ACCESSION CODE EU293536, AND IT WILL BE LOCATED IN UNIPROTKB LATER.

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M (NH4)2SO4, 0.1M NaCacodylate, pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.58→52.71 Å / Num. all: 81449 / Num. obs: 81449 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.4
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.7 / Num. unique all: 11879 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z7A

1z7a


Resolution: 1.58→9.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.911 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; ARG 167 side chain is in alternate conformations
RfactorNum. reflection% reflectionSelection details
Rfree0.23248 4064 5 %RANDOM
Rwork0.2077 ---
obs0.20896 77048 99.84 %-
all-77048 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.649 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.58→9.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 0 292 5246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9396937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38822.747273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96515813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5461549
X-RAY DIFFRACTIONr_chiral_restr0.0780.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024063
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.32243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.53497
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5554
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.3145
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.565
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.123090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65134862
X-RAY DIFFRACTIONr_scbond_it1.31822312
X-RAY DIFFRACTIONr_scangle_it1.90132070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 279 -
Rwork0.273 5628 -
obs--99.92 %

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