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- PDB-4a42: CpGH89CBM32-6 produced by Clostridium perfringens -

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Basic information

Entry
Database: PDB / ID: 4a42
TitleCpGH89CBM32-6 produced by Clostridium perfringens
ComponentsALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
KeywordsHYDROLASE / FAMILY 89 GLYCOSIDE HYDROLASE / FAMILY 32 CARBOHYDRATE-BINDING MODULE / CPF_0859
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alpha-N-acetylglucosaminidase / Alpha-N-acetylglucosaminidase, N-terminal / Alpha-N-acetylglucosaminidase, C-terminal / Alpha-N-acetylglucosaminidase, tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain / Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain / FIVAR domain / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. ...Alpha-N-acetylglucosaminidase / Alpha-N-acetylglucosaminidase, N-terminal / Alpha-N-acetylglucosaminidase, C-terminal / Alpha-N-acetylglucosaminidase, tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain / Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain / FIVAR domain / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-N-acetylglucosaminidase family protein / Probable alpha-N-acetylglucosaminidase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsFicko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B.
CitationJournal: Plos One / Year: 2012
Title: Carbohydrate Recognition by an Architecturally Complex Alpha-N-Acetylglucosaminidase from Clostridium Perfringens.
Authors: Ficko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B.
History
DepositionOct 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
B: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7264
Polymers33,6462
Non-polymers802
Water3,135174
1
A: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8632
Polymers16,8231
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8632
Polymers16,8231
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.810, 48.810, 98.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN / GH89_CBM32-4


Mass: 16823.033 Da / Num. of mol.: 2 / Fragment: CBM32-4, RESIDUES 1496-1621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0TST1, UniProt: Q8XM24*PLUS, alpha-N-acetylglucosaminidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSELENOMETHIONINE DERIVATIVE

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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: 1.74 Å3/Da / Density % sol: 29.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 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: 1.55→30 Å / Num. obs: 33037 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 15.2 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.6
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 7.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.55→28.234 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 22.78 / Stereochemistry target values: ML
Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY AND RESIDUES WITH POOR SIDE CHAIN DENSITY ARE PRESENTED AS STUBS.
RfactorNum. reflection% reflection
Rfree0.2387 1668 5.1 %
Rwork0.1966 --
obs0.1988 33037 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.2 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7346 Å20 Å20 Å2
2--0.7346 Å20 Å2
3----1.4692 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 2 174 2083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112037
X-RAY DIFFRACTIONf_angle_d1.2942783
X-RAY DIFFRACTIONf_dihedral_angle_d13.614762
X-RAY DIFFRACTIONf_chiral_restr0.089317
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59560.28951410.20842552X-RAY DIFFRACTION97
1.5956-1.64710.23871280.19732578X-RAY DIFFRACTION98
1.6471-1.7060.27431390.18812589X-RAY DIFFRACTION99
1.706-1.77430.20111370.18152592X-RAY DIFFRACTION99
1.7743-1.8550.25361620.1862595X-RAY DIFFRACTION99
1.855-1.95280.23281470.18552645X-RAY DIFFRACTION100
1.9528-2.07510.21191310.1772592X-RAY DIFFRACTION100
2.0751-2.23530.26981280.19472666X-RAY DIFFRACTION100
2.2353-2.46010.25381400.19672621X-RAY DIFFRACTION100
2.4601-2.81580.26931280.2142644X-RAY DIFFRACTION100
2.8158-3.54650.26171340.20332641X-RAY DIFFRACTION100
3.5465-28.23870.20221530.1962654X-RAY DIFFRACTION99

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