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- PDB-5gzt: Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. F... -

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Basic information

Entry
Database: PDB / ID: 5gzt
TitleCrystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery
Components(Chitinase) x 2
KeywordsHYDROLASE
Function / homology
Function and homology information


chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Chitinase W immunoglobulin-like domain / Chitinase W immunoglobulin-like domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II ...Chitinase W immunoglobulin-like domain / Chitinase W immunoglobulin-like domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
FORMIC ACID / PHOSPHATE ION / Chitinase
Similarity search - Component
Biological speciesPaenibacillus sp. FPU-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsItoh, T. / Hibi, T. / Suzuki, F. / Sugimoto, I. / Fujiwara, A. / Inaka, K. / Tanaka, H. / Ohta, K. / Fujii, Y. / Taketo, A. / Kimoto, H.
CitationJournal: PLoS ONE / Year: 2016
Title: Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery
Authors: Itoh, T. / Hibi, T. / Suzuki, F. / Sugimoto, I. / Fujiwara, A. / Inaka, K. / Tanaka, H. / Ohta, K. / Fujii, Y. / Taketo, A. / Kimoto, H.
History
DepositionOct 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Derived calculations
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,40114
Polymers134,8222
Non-polymers57812
Water24,4641358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-24 kcal/mol
Surface area48250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.339, 123.486, 130.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Chitinase


Mass: 11373.742 Da / Num. of mol.: 1 / Fragment: UNP residues 198-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FPU-7 (bacteria) / Gene: chiW / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7ZLW6
#2: Protein Chitinase


Mass: 123448.656 Da / Num. of mol.: 1 / Fragment: UNP residues 283-1418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FPU-7 (bacteria) / Gene: chiW / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7ZLW6

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Non-polymers , 4 types, 1370 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1358 / 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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 297 K / Method: small tubes / pH: 5.5 / Details: (NH4)2HPO4, Na-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50.01 Å / Num. obs: 108304 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 50.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 4.42 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1itx

1itx


Resolution: 2.1→50.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.845 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 5370 5 %RANDOM
Rwork0.17535 ---
obs0.17762 102679 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20 Å2
2--0.33 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9185 0 36 1358 10579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.029455
X-RAY DIFFRACTIONr_bond_other_d0.0020.028801
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.94912861
X-RAY DIFFRACTIONr_angle_other_deg1.093320282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48851213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86225.038399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.531151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0111529
X-RAY DIFFRACTIONr_chiral_restr0.1190.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210883
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022124
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_it3.7463.6344822
X-RAY DIFFRACTIONr_mcbond_other3.7463.6344823
X-RAY DIFFRACTIONr_mcangle_it5.345.4326027
X-RAY DIFFRACTIONr_mcangle_other5.345.4336028
X-RAY DIFFRACTIONr_scbond_it3.8033.7574633
X-RAY DIFFRACTIONr_scbond_other3.7613.7554610
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.575.5266829
X-RAY DIFFRACTIONr_long_range_B_refined7.99442.73511362
X-RAY DIFFRACTIONr_long_range_B_other7.83442.26610993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 393 -
Rwork0.215 7446 -
obs--98.68 %

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