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- PDB-2wly: Chitinase A from Serratia marcescens ATCC990 in complex with Chit... -

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Basic information

Entry
Database: PDB / ID: 2wly
TitleChitinase A from Serratia marcescens ATCC990 in complex with Chitotrio-thiazoline.
ComponentsChitinase
KeywordsHYDROLASE / THIAZOLINES / CHITINASE A / GLYCOSIDASE / CHITIN HYDROLYSIS / CHITIN DEGRADATION / POLYSACCHARIDE DEGRADATION / FAMILY 18 CHITINASES / CARBOHYDRATE METABOLISM
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / 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 / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Roll / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Chem-NGT / DI(HYDROXYETHYL)ETHER / Chem-SN5 / Chitinase / Chitinase A
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTaylor, E.J. / Dennis, R.J. / Macdonald, J.M. / Tarling, C.A. / Knapp, S. / Withers, S.G. / Davies, G.J.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2010
Title: Chitinase inhibition by chitobiose and chitotriose thiazolines.
Authors: Macdonald, J.M. / Tarling, C.A. / Taylor, E.J. / Dennis, R.J. / Myers, D.S. / Knapp, S. / Davies, G.J. / Withers, S.G.
History
DepositionJun 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Dec 12, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_ec / _entity.src_method
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,97211
Polymers59,7571
Non-polymers1,21510
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.004, 201.442, 59.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Chitinase


Mass: 59756.781 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6XFF7, UniProt: P07254*PLUS
#4: Sugar ChemComp-SN5 / 2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose / N-ethanethioyl-beta-D-glucosamine / 2-deoxy-2-(ethanethioylamino)-beta-D-glucose / 2-deoxy-2-(ethanethioylamino)-D-glucose / 2-deoxy-2-(ethanethioylamino)-glucose


Type: D-saccharide, beta linking / Mass: 237.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO5S

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Non-polymers , 4 types, 335 molecules

#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHERE ARE KNOWN DISCREPANCIES IN THE SEQUENCE DEPENDING ON WHICH STRAIN OF SERRATIA MARCESCENS THE ...THERE ARE KNOWN DISCREPANCIES IN THE SEQUENCE DEPENDING ON WHICH STRAIN OF SERRATIA MARCESCENS THE CLONE WAS DERIVED FROM. THE BEST MATCH IS USING SEQUENCE ABI58232.1. THIS WAS DERIVED FROM ATCC 990. WE HAVE SEQUENCED THIS GENE FROM TWO INDEPENDENT PCR REACTIONS USING A GENOMIC DNA TEMPLATE AND FOUND THEM TO BE IDENTICAL. THE STRAINS 2170, 27117, BJL200, ATCC990 AND QMB1466 ARE SAID TO BE IDENTICAL THIS MAY NOT BE THE CASE. THE ORIGINAL SEQUENCE HAD A N-TERMINAL SIGNAL PEPTIDE WHICH IS DERIVED FROM THE EXPRESSION VECTOR PET 22B. THIS IS CLEAVED OFF. THERE IS A C-TERMINAL HISTIDINE TAG WHICH IS DISORDERED IN THE STRUCTURE.

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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: 3.38 Å3/Da / Density % sol: 63.62 % / Description: NONE
Crystal growpH: 8
Details: 1.0M SODIUM CITRATE 10MM SODIUM BORATE PH8 DIOXANE 20%, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 30934 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0097refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDQ

1edq


Resolution: 2.4→109.76 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.528 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20486 1558 5 %RANDOM
Rwork0.1551 ---
obs0.15771 29370 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→109.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 79 326 4529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9545853
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69225.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33615675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8971512
X-RAY DIFFRACTIONr_chiral_restr0.1360.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213290
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_it1.0891.52667
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9624261
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.44731656
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3384.51591
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.397→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 96 -
Rwork0.218 2134 -
obs--97.64 %

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