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

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Basic information

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


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
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 / Glyco_18 ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Chitinase
Similarity search - Component
Biological speciesPaenibacillus sp. FPU-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 1.1Feb 26, 2020Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,8106
Polymers196,7712
Non-polymers1,0394
Water3,639202
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9053
Polymers98,3861
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-6 kcal/mol
Surface area34220 Å2
MethodPISA
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9053
Polymers98,3861
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area33940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.989, 127.229, 161.406
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 Chitinase


Mass: 98385.656 Da / Num. of mol.: 2 / Fragment: UNP residues 557-1418
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
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: (NH4)2HPO4, Na-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50.01 Å / Num. obs: 70506 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 41.44
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.08 / % possible all: 99.2

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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: 2.61→50.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.109 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.582 / ESU R Free: 0.306 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25343 3459 4.9 %RANDOM
Rwork0.20263 ---
obs0.20514 66976 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.61→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13479 0 68 202 13749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213923
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212766
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.94718984
X-RAY DIFFRACTIONr_angle_other_deg1.076329397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.91751725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41724.719640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.364152172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3551549
X-RAY DIFFRACTIONr_chiral_restr0.0970.22070
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115980
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023245
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_it3.5864.3456882
X-RAY DIFFRACTIONr_mcbond_other3.5864.3446881
X-RAY DIFFRACTIONr_mcangle_it5.626.5088601
X-RAY DIFFRACTIONr_mcangle_other5.6196.5088602
X-RAY DIFFRACTIONr_scbond_it3.1934.5257041
X-RAY DIFFRACTIONr_scbond_other3.1914.5257038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0936.68310374
X-RAY DIFFRACTIONr_long_range_B_refined7.73550.21415771
X-RAY DIFFRACTIONr_long_range_B_other7.73350.21415765
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.613→2.681 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 222 -
Rwork0.275 4534 -
obs--91.97 %

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