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- PDB-4qwp: co-crystal structure of chitosanase OU01 with substrate -

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Basic information

Entry
Database: PDB / ID: 4qwp
Titleco-crystal structure of chitosanase OU01 with substrate
ComponentsChitosanase
KeywordsHYDROLASE / chitosan / glycoside hydrolase / Chitosanase OU01 / chito-oligomer / hydrolysis
Function / homology
Function and homology information


chitosanase / chitosanase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitosanase; Chain A, domain 2 / Chitosanase, subunit A, domain 2 / Chitosanases families 46 and 80 active sites signature. / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily / Up-down Bundle ...Chitosanase; Chain A, domain 2 / Chitosanase, subunit A, domain 2 / Chitosanases families 46 and 80 active sites signature. / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chitosanase
Similarity search - Component
Biological speciesPseudomonas sp. A-01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLyu, Q. / Liu, W. / Han, B.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Structural and biochemical insights into the degradation mechanism of chitosan by chitosanase OU01.
Authors: Lyu, Q. / Shi, Y. / Wang, S. / Yang, Y. / Han, B. / Liu, W. / Jones, D.N. / Liu, W.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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: Chitosanase
B: Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1198
Polymers53,1232
Non-polymers1,9966
Water6,539363
1
A: Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4634
Polymers26,5621
Non-polymers9013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6574
Polymers26,5621
Non-polymers1,0953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.235, 40.885, 105.313
Angle α, β, γ (deg.)90.00, 106.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chitosanase /


Mass: 26561.664 Da / Num. of mol.: 2 / Fragment: chitosanase OU01 / Mutation: Asp43Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. A-01 (bacteria) / Strain: Microbacterium sp. / Gene: chitosanase OU01 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q8KZM5, chitosanase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 340.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*N]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2- ...2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 501.483 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*N]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 365 molecules

#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTALLIZED SEQUENCE REFERS TO CHITOSANASE OU01 DERIVED FROM THE MICROBACTERIUM SP. OU01 WITH ...THE CRYSTALLIZED SEQUENCE REFERS TO CHITOSANASE OU01 DERIVED FROM THE MICROBACTERIUM SP. OU01 WITH GENBANK ACCESSION: ABM91442. THE CORRECT SEQUENCE DESCRIPTION IS INDICATED IN THE MANUSCRIPT AS BELOW(LYQ. ET. AL., BIOCHEMICAL JOURNAL,. 461(2):335-45). THE AMINO ACID SEQUENCE ENCODED BY THE CLONED CHITOSANASE OU01 GENE HAD THREE DIFFERENT RESIDUES. (COMPARED TO THE PREVIOUS SUBMITTED CHITOSANASE OU01 SEQUENCE (GENBANK ACCESSION: ABM91442), RESIDUES IN POSITION 68, 91 AND 237 ARE TYR, ASP AND TYR, RESPECTIVELY, HOWEVER, IN THIS STUDY, THE CORRESPONDING RESIDUES ARE HIS, GLY AND PHE.

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 290 K
Details: 0.05 M KH2PO4, 23% PEG 8000 using 0.7 M NaCl as the reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97869
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 53026 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OLT

4olt


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.492 / SU ML: 0.059 / Isotropic thermal model: 0.2047 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2765 5.1 %RANDOM
Rwork0.166 ---
obs0.168 51607 96.9 %-
all-53832 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0.06 Å2
2--0.05 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 132 363 4093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193922
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9785339
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3755494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55324.472199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01115547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8311527
X-RAY DIFFRACTIONr_chiral_restr0.1380.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213093
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_it1.1951.2071950
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7441.7982452
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3071.4941972
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.89211.5686511
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 195 -
Rwork0.203 3411 -
obs--88.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1894-0.0796-1.09950.86850.77593.35440.04610.0208-0.0694-0.00790.02780.00470.1477-0.0742-0.0740.0612-0.0106-0.01130.0241-0.0160.042245.329-6.09362.642
20.9568-0.4316-0.4411.25420.63820.7140.04650.2077-0.0075-0.0278-0.07530.02430.0239-0.1770.02870.0151-0.01870.01070.1266-0.02340.017424.5823.79564.296
35.24292.4039-1.08813.0455-0.38882.9731-0.09760.1181-0.04420.0357-0.06250.08710.2581-0.22580.160.0462-0.03780.00770.1079-0.05390.05428.386-5.60558.173
40.854-0.29480.06240.56540.37561.46820.02750.06370.0341-0.05250.0002-0.0395-0.1242-0.0125-0.02760.0532-0.00680.01250.0299-00.026148.1988.07957.97
53.9702-1.8309-2.91550.89241.27533.9685-0.0015-0.03460.1460.02680.0495-0.1006-0.12110.0368-0.0480.0549-0.0083-0.01120.04-0.02740.034553.39810.77566.465
61.6813-1.0339-1.15851.31551.0132.064-0.0532-0.08470.03680.04950.1081-0.03930.09170.1575-0.05490.04720.005-0.02350.0327-0.01980.025754.4520.42869.15
71.9459-1.2274-1.2833.87272.61153.9536-0.1081-0.1525-0.22350.26370.1155-0.06120.32440.0591-0.00740.09160.0033-0.02390.01480.02290.064349.577-8.09172.099
81.3633-1.1003-0.76931.19250.99692.14540.0033-0.0309-0.03670.05360.0486-0.0305-0.00770.0644-0.05190.0539-0.0082-0.00510.0064-0.00260.05163.7816.59194.299
91.56320.281-0.52510.4835-0.34071.55150.0303-0.02830.11960.04370.0074-0.0161-0.02550.102-0.03780.0148-0.00320.01170.0314-0.03290.053384.28612.11887.301
103.9588-2.5860.97515.6064-2.38773.54890.0297-0.06520.03830.132-0.1038-0.04460.23020.14980.0740.04040.00120.00610.0513-0.02160.027481.4837.23298.263
111.0683-0.22710.05620.4750.25740.6959-0.0160.02950.0262-0.06830.0314-0.0135-0.15140.018-0.01550.0817-0.00440.0010.0043-0.00110.043861.79320.89290.135
122.39630.0099-0.97041.38711.25062.1561-0.13540.1452-0.0617-0.1886-0.00890.1062-0.16-0.1160.14440.08020.0089-0.02280.03190.00860.032952.04719.91884.14
134.8211.1096-6.07194.36730.51788.55-0.1316-0.16050.09950.13610.22560.0550.2710.3084-0.0940.102-0.04470.0190.0767-0.01460.059265.49315.82873.143
141.01530.0391-0.14390.52950.45451.0594-0.03480.0875-0.0686-0.0131-0.01040.03890.0135-0.09790.04530.0505-0.0082-0.01090.017-0.00340.03155.9984.83386.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 31
2X-RAY DIFFRACTION2A32 - 108
3X-RAY DIFFRACTION3A109 - 120
4X-RAY DIFFRACTION4A121 - 177
5X-RAY DIFFRACTION5A178 - 203
6X-RAY DIFFRACTION6A204 - 224
7X-RAY DIFFRACTION7A225 - 240
8X-RAY DIFFRACTION8B5 - 31
9X-RAY DIFFRACTION9B32 - 108
10X-RAY DIFFRACTION10B109 - 117
11X-RAY DIFFRACTION11B118 - 177
12X-RAY DIFFRACTION12B178 - 196
13X-RAY DIFFRACTION13B197 - 203
14X-RAY DIFFRACTION14B204 - 240

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