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- PDB-1ur9: Interactions of a family 18 chitinase with the designed inhibitor... -

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Basic information

Entry
Database: PDB / ID: 1ur9
TitleInteractions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone
ComponentsCHITINASE B
KeywordsHYDROLASE / CHITINASE / INHIBITION / LACTONE / CHITIN DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module superfamily 5/12 / Seminal Fluid Protein PDC-109 (Domain B) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily ...Carbohydrate-binding module superfamily 5/12 / Seminal Fluid Protein PDC-109 (Domain B) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-[(AMINOOXY)CARBONYL]-N-PHENYLAMINE / chitinase
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVaaje-Kolstad, G. / Vasella, A. / Peter, M.G. / Netter, C. / Houston, D.R. / Westereng, B. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Interactions of a Family 18 Chitinase with the Designed Inhibitor Hm508 and its Degradation Product, Chitobiono-Delta-Lactone.
Authors: Vaaje-Kolstad, G. / Vasella, A. / Peter, M.G. / Netter, C. / Houston, D.R. / Westereng, B. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural Insights Into the Catalytic Mechansim of a Family 18 Exochitinase
Authors: Van Aalten, D.M.F. / Komander, D. / Synstad, B. / Gaseidnes, S. / Peter, M.G. / Eijsink, V.G.H.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structure of a Two-Domain Chitotriosidase from Serratia Marcescens at 1.9 A Resolution
Authors: Van Aalten, D.M.F. / Synstad, B. / Brurberg, M.B. / Hough, E. / Riise, B. / Eijsink, V.G.H. / Wierenga, R.K.
History
DepositionOct 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHITINASE B
B: CHITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,11479
Polymers111,2062
Non-polymers7,90877
Water15,385854
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20420 Å2
ΔGint-140.9 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.524, 104.177, 185.992
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 / Sugars , 2 types, 4 molecules AB

#1: Protein CHITINASE B


Mass: 55603.145 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: BJL200 / Description: CLONED GENE / Production host: ESCHERICHIA COLI DH5[ALPHA] (bacteria) / References: UniProt: Q54276, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone


Type: oligosaccharide / Mass: 422.385 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[A2122h_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 929 molecules

#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PHJ / N-[(AMINOOXY)CARBONYL]-N-PHENYLAMINE / N-[(AMINOOXY)CARBONYL]ANILINE


Mass: 152.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION ASP 142 ASN
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growpH: 7
Details: 100 MM HEPES PH 7.0, 15% GLYCEROL, 1.3 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.86
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 97967 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.7 / % possible all: 77.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOI

1goi


Resolution: 1.8→24.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2048263.85 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME SIDECHAIN ATOMS HAVE BEEN OMITTED DUE TO MISSING OR AMBIGUOUS ELECTRON DENSITY. THESE ATOMS ARE LISTED IN REMARK 470
RfactorNum. reflection% reflectionSelection details
Rfree0.255 983 1 %RANDOM
Rwork0.208 ---
obs0.208 97878 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.0995 Å2 / ksol: 0.338994 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20 Å2
2--5.21 Å20 Å2
3----6.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7804 0 507 854 9165
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.612.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 165 1.2 %
Rwork0.31 13766 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP

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