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- PDB-3ren: CPF_2247, a novel alpha-amylase from Clostridium perfringens -

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Basic information

Entry
Database: PDB / ID: 3ren
TitleCPF_2247, a novel alpha-amylase from Clostridium perfringens
ComponentsGlycosyl hydrolase, family 8Glycoside hydrolase
KeywordsHYDROLASE / (alpha/alpha)6-barrel fold / alpha-amylase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / membrane => GO:0016020 / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycosyl hydrolase, family 8 / Glycosyl hydrolase, family 8
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFicko-Blean, E. / Stuart, C.P. / Boraston, A.B.
CitationJournal: Proteins / Year: 2011
Title: Structural analysis of CPF_2247, a novel alpha-amylase from Clostridium perfringens.
Authors: Ficko-Blean, E. / Stuart, C.P. / Boraston, A.B.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase, family 8
B: Glycosyl hydrolase, family 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,30121
Polymers81,1332
Non-polymers1,16819
Water10,665592
1
A: Glycosyl hydrolase, family 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,14511
Polymers40,5661
Non-polymers57910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycosyl hydrolase, family 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,15510
Polymers40,5661
Non-polymers5899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.350, 75.060, 158.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl hydrolase, family 8 / Glycoside hydrolase


Mass: 40566.289 Da / Num. of mol.: 2 / Fragment: unp residues 43-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CPF_2247 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0TNX0, UniProt: A0A0H2YP60*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 49752 / Num. obs: 49752 / Observed criterion σ(I): 2

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Processing

SoftwareName: REFMAC / Version: 5.5.0072 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.909 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22383 2524 5.1 %RANDOM
Rwork0.16931 ---
obs0.17208 47079 92.64 %-
all-49752 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 70 592 6025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225546
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9647479
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3215693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45925.589263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96315976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6731514
X-RAY DIFFRACTIONr_chiral_restr0.1040.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024143
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8631.53360
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59925404
X-RAY DIFFRACTIONr_scbond_it2.66532186
X-RAY DIFFRACTIONr_scangle_it4.2364.52063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 134 -
Rwork0.23 2456 -
obs--66.19 %

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