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- PDB-3afb: Crystal structures of catalytic site mutants of active domain 2 o... -

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Basic information

Entry
Database: PDB / ID: 3afb
TitleCrystal structures of catalytic site mutants of active domain 2 of chitinase from Pyrococcus furiosus
ComponentsPutative chitinase
KeywordsHYDROLASE / (beta/alpha)8-barrel
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / polysaccharide binding / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / : / CBM2/CBM3, carbohydrate-binding domain superfamily / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / : / CBM2/CBM3, carbohydrate-binding domain superfamily / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsTsuji, H.
CitationJournal: Febs J. / Year: 2010
Title: Kinetic and crystallographic analyses of the catalytic domain of chitinase from Pyrococcus furiosus- the role of conserved residues in the active site
Authors: Tsuji, H. / Nishimura, S. / Inui, T. / Kado, Y. / Ishikawa, K. / Nakamura, T. / Uegaki, K.
History
DepositionFeb 25, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative chitinase
B: Putative chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9539
Polymers69,4402
Non-polymers5137
Water8,539474
1
A: Putative chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0215
Polymers34,7201
Non-polymers3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9334
Polymers34,7201
Non-polymers2123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.912, 91.997, 107.402
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 Putative chitinase


Mass: 34720.215 Da / Num. of mol.: 2 / Fragment: catalytic domain (AD2), UNP residues 409-717 / Mutation: D524A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1233 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1H5, chitinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.54 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 88365 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.1
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→46.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.481 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18232 4395 5 %RANDOM
Rwork0.16113 ---
obs0.1622 83365 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.146 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.76→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 31 474 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.956866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0315623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71824.41229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32615784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2361518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023894
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22497
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23525
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2385
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined1.420.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8231.53133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16524954
X-RAY DIFFRACTIONr_scbond_it2.0232218
X-RAY DIFFRACTIONr_scangle_it3.214.51904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.764→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 324 -
Rwork0.195 5827 -
obs--95.82 %

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