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- PDB-3cl8: Crystal structure of Puue Allantoinase complexed with ACA -

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Basic information

Entry
Database: PDB / ID: 3cl8
TitleCrystal structure of Puue Allantoinase complexed with ACA
ComponentsPuue Allantoinase
KeywordsHYDROLASE / Allantoine / Allantoinase / uric acid degradation / amino imidazole carboximide
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
5-amino-1H-imidazole-4-carboxamide / NodB homology domain-containing protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Puue Allantoinase
B: Puue Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1884
Polymers70,9362
Non-polymers2522
Water2,450136
1
A: Puue Allantoinase
hetero molecules

A: Puue Allantoinase
hetero molecules

A: Puue Allantoinase
hetero molecules

A: Puue Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3778
Polymers141,8724
Non-polymers5044
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 area15160 Å2
ΔGint-23 kcal/mol
Surface area39520 Å2
MethodPISA
2
B: Puue Allantoinase
hetero molecules

B: Puue Allantoinase
hetero molecules

B: Puue Allantoinase
hetero molecules

B: Puue Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3778
Polymers141,8724
Non-polymers5044
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area15310 Å2
ΔGint-24 kcal/mol
Surface area38520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.723, 97.723, 61.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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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: Chemical ChemComp-5AC / 5-amino-1H-imidazole-4-carboxamide


Mass: 126.117 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→69.2 Å / Num. all: 24175 / Num. obs: 24175 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 9
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3346 / % possible all: 83.6

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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 3CL6

3cl6


Resolution: 2.25→69.1 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.602 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.692 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22967 1213 5 %RANDOM
Rwork0.2067 ---
obs0.20784 22962 87.38 %-
all-22962 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.549 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---1.47 Å20 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.25→69.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4938 0 18 136 5092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9436935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9065608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38622.841271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.44315807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4231547
X-RAY DIFFRACTIONr_chiral_restr0.0740.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024067
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2740.32869
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.53406
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.5399
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.3199
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.530
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.50523062
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.46534850
X-RAY DIFFRACTIONr_scbond_it6.33722321
X-RAY DIFFRACTIONr_scangle_it8.34532082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 76 -
Rwork0.298 1470 -
obs--77.22 %

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