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- PDB-1w1p: Crystal structure of S. marcescens chitinase B in complex with th... -

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Basic information

Entry
Database: PDB / ID: 1w1p
TitleCrystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(Gly-L-Pro) at 2.1 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-(GLYCINE-L-PROLINE) INHIBITOR / chitinase
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 6, 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)113,76330
Polymers111,0362
Non-polymers2,72728
Water17,096949
1
A: CHITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,61423
Polymers55,5181
Non-polymers2,09622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CHITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1497
Polymers55,5181
Non-polymers6316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.070, 103.906, 186.439
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.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-GIO / CYCLO-(GLYCINE-L-PROLINE) INHIBITOR / (8AR)-HEXAHYDROPYRROLO[1,2-A]PYRAZINE-1,4-DIONE


Mass: 154.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N2O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / 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: 2.47 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: 2.1→20 Å / Num. obs: 57855 / % possible obs: 89.7 % / Observed criterion σ(I): 1 / Redundancy: 3.22 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.79
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.3 / % possible all: 90.9

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Processing

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

1o6i


Resolution: 2.1→24.91 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2543996.39 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.249 581 1 %RANDOM
Rwork0.199 ---
obs0.199 57797 48.1 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 53.9279 Å2 / ksol: 0.334367 e/Å3
Displacement parametersBiso mean: 29.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--3.18 Å20 Å2
3----4.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7815 0 172 949 8936
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009586
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_deg1.45177
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_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it2.862.5

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