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- PDB-8hfd: Crystal structure of allantoinase from E. coli BL21 -

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Basic information

Entry
Database: PDB / ID: 8hfd
TitleCrystal structure of allantoinase from E. coli BL21
ComponentsAllantoinase
KeywordsHYDROLASE / allantoinase / allantoin
Function / homology
Function and homology information


allantoinase / allantoin catabolic process / allantoinase activity / cobalt ion binding / purine nucleobase metabolic process / zinc ion binding
Similarity search - Function
: / Allantoinase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Allantoinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLin, E.S. / Huang, H.Y. / Yang, P.C. / Liu, H.W. / Huang, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2023
Title: Crystal Structure of Allantoinase from Escherichia coli BL21: A Molecular Insight into a Role of the Active Site Loops in Catalysis.
Authors: Huang, Y.H. / Yang, P.C. / Lin, E.S. / Ho, Y.Y. / Peng, W.F. / Lu, H.P. / Huang, C.C. / Huang, C.Y.
History
DepositionNov 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allantoinase
B: Allantoinase
C: Allantoinase
D: Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,40118
Polymers202,2414
Non-polymers1,16014
Water16,682926
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-328 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.158, 77.142, 144.847
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Allantoinase / Allantoin-utilizing enzyme


Mass: 50560.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: allB, BMT91_19075, E2127_17875, E2128_18450, E2132_17365, E4T14_14655, E6D34_22765, ELT21_17110
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V3VVF3, allantoinase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 20% PEG8000, 100 mM CHES, pH9.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→30 Å / Num. obs: 132819 / % possible obs: 99.02 % / Redundancy: 3.5 % / CC1/2: 0.992 / Net I/σ(I): 7.39
Reflection shellResolution: 2.07→2.19 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 12965 / CC1/2: 0.855 / % possible all: 97.21

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.19.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+74 / Resolution: 2.07→29.92 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1996 1.5 %
Rwork0.2051 --
obs0.2057 132805 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13783 0 50 926 14759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914139
X-RAY DIFFRACTIONf_angle_d0.97719091
X-RAY DIFFRACTIONf_dihedral_angle_d7.8141952
X-RAY DIFFRACTIONf_chiral_restr0.0592107
X-RAY DIFFRACTIONf_plane_restr0.0092525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.120.25831370.21849009X-RAY DIFFRACTION96
2.12-2.180.28031440.21749384X-RAY DIFFRACTION100
2.18-2.240.2711430.21279320X-RAY DIFFRACTION100
2.24-2.320.26971430.21029399X-RAY DIFFRACTION100
2.32-2.40.26671430.21089386X-RAY DIFFRACTION100
2.4-2.50.2621430.20999368X-RAY DIFFRACTION100
2.5-2.610.29591420.20649377X-RAY DIFFRACTION100
2.61-2.750.23161440.20339361X-RAY DIFFRACTION100
2.75-2.920.25461440.21059348X-RAY DIFFRACTION100
2.92-3.140.25751410.2199357X-RAY DIFFRACTION99
3.14-3.460.23131420.21079264X-RAY DIFFRACTION98
3.46-3.960.2241400.19449321X-RAY DIFFRACTION98
3.96-4.980.23491440.18269356X-RAY DIFFRACTION98
4.98-29.920.25611460.21619559X-RAY DIFFRACTION99

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