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- PDB-1goi: Crystal structure of the D140N mutant of chitinase B from Serrati... -

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Basic information

Entry
Database: PDB / ID: 1goi
TitleCrystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 A resolution
ComponentsCHITINASE B
KeywordsHYDROLASE / CHITIN DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


endochitinase activity / 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 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / 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 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / 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 (GH18) domain profile. / Glycosyl hydrolases family 18 / 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
Chitinase B / chitinase
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKolstad, G. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the D140N Mutant of Chitinase B from Serratia Marcescens at 1.45 A Resolution.
Authors: Kolstad, G. / 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 Exo-Chitinase
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 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / 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 1.3Oct 23, 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" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY AN 10-STRANDED BARREL THESE ARE REPRESENTED BY A 11-STRANDED SHEETS 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)112,52318
Polymers111,0342
Non-polymers1,48916
Water18,0151000
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-51.5 kcal/mol
Surface area37180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.904, 104.016, 186.524
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: 55517.027 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) SERRATIA MARCESCENS (bacteria) / Strain: BJL200
References: UniProt: Q54276, UniProt: P11797*PLUS, chitinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1000 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION ASP140ASN HYDROLYSIS OF THE 1,4-BETA-LINKAGES OF N-ACETYL-D- ...CHAIN A, B ENGINEERED MUTATION ASP140ASN HYDROLYSIS OF THE 1,4-BETA-LINKAGES OF N-ACETYL-D-GLUCOSAMINE POLYMERS OF CHITIN.
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: 2.09 Å3/Da / Density % sol: 41.3 %
Crystal growpH: 7
Details: 100 MM HEPES, 1.25 M AMMONIUM SULPHATE, 10% GLYCEROL, pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %glycerol1reservoir
31.25 Mammonium sulfate1reservoir
4100 mMHEPES1reservoirpH7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.45→17 Å / Num. obs: 191634 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.7
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 17 Å / Num. measured all: 600078
Reflection shell
*PLUS
Lowest resolution: 1.5 Å / % possible obs: 99.5 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E15

1e15


Resolution: 1.45→17 Å / Num. parameters: 80913 / Num. restraintsaints: 100084 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 1921 1 %RANDOM
obs0.1601 -99.3 %-
all-191433 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 7279 / Occupancy sum non hydrogen: 8885.5
Refinement stepCycle: LAST / Resolution: 1.45→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7793 0 92 1000 8885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0261
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.028
X-RAY DIFFRACTIONs_approx_iso_adps0.088
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.1601
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.32
X-RAY DIFFRACTIONs_plane_restr0.0261
X-RAY DIFFRACTIONs_chiral_restr0.029

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