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- PDB-1w1t: Crystal structure of S. marcescens chitinase B in complex with th... -

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Basic information

Entry
Database: PDB / ID: 1w1t
TitleCrystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(His-L-Pro) at 1.9 A resolution
ComponentsCHITINASE B
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / CHITINASE / STRUCTURE-BASED INHIBITOR DESIGN / CYCLIC DIPEPTIDE
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
CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR / chitinase
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHouston, D.R. / Synstad, B. / Eijsink, V.G.H. / Eggleston, I. / van Aalten, D.M.F.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Structure-Based Exploration of Cyclic Dipeptide Chitinase Inhibitors
Authors: Houston, D.R. / Synstad, B. / Eijsink, V.G.H. / Stark, M.J. / Eggleston, I. / Van Aalten, D.M.F.
History
DepositionJun 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,29931
Polymers111,0362
Non-polymers3,26329
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-74.2 kcal/mol
Surface area36060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.845, 103.975, 186.016
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 B


Mass: 55518.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q54276, chitinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CHQ / CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR / (3S,8AR)-3-(1H-IMIDAZOL-5-YLMETHYL)HEXAHYDROPYRROLO[1,2-A]PYRAZINE-1,4-DIONE


Mass: 234.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49 %
Crystal growpH: 7
Details: 1.5 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7, 25 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 85317 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.41 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.91
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.31 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O6I

1o6i


Resolution: 1.9→24.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2669843.24 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.222 846 1 %RANDOM
Rwork0.193 ---
obs0.193 85077 98.7 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 48.6515 Å2 / ksol: 0.356394 e/Å3
Displacement parametersBiso mean: 29.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.94 Å20 Å20 Å2
2--4.71 Å20 Å2
3----8.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7803 0 212 780 8795
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_deg1.53
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellHighest resolution: 1.9 Å

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