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- PDB-1o6i: Chitinase B from Serratia marcescens complexed with the catalytic... -

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Basic information

Entry
Database: PDB / ID: 1o6i
TitleChitinase B from Serratia marcescens complexed with the catalytic intermediate mimic cyclic dipeptide CI4.
ComponentsChitinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / CHITINASE / CATALYTIC INTERMEDIATE MIMIC / CYCLIC DIPEPTIDE / HYDROLASE- HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / 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 / Chitinase II ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-0HZ / Chitinase B / Chitinase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHouston, D.R. / Eggleston, I. / Synstad, B. / Eijsink, V.G.H. / van Aalten, D.M.F.
CitationJournal: Biochem. J. / Year: 2002
Title: The cyclic dipeptide CI-4 [cyclo-(l-Arg-d-Pro)] inhibits family 18 chitinases by structural mimicry of a reaction intermediate.
Authors: Houston, D.R. / Eggleston, I. / Synstad, B. / Eijsink, V.G. / van Aalten, D.M.
History
DepositionOct 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other
Revision 1.4Jun 13, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct_ref
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
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: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,97641
Polymers111,0362
Non-polymers3,94039
Water25,5091416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.805, 103.743, 186.283
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


Mass: 55518.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q54276, UniProt: P11797*PLUS
#2: Chemical ChemComp-0HZ / amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium / CI-4 / [cyclo-(l-Arg-d-Pro)]


Type: peptide-like / Mass: 254.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N5O2
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 1416 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES THE HYDROLYSIS OF THE 1,4-BETA-LINKAGES OF THE NAG POLYMERS OF CHITIN.
Nonpolymer detailsCYCLIC PEPTIDE IN CHAINS A AND B COMPOSED OF D-PROLINE AND L-ARGININE

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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: 47.99 %
Crystal growpH: 7
Details: 1.4M AMMONIUM SULPHATE 0.1M HEPES PH 7.0, 25% GLYCEROL
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Details: van Aalten, D.M.F., (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 5842.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMcitrate1reservoir
30.5 M1reservoirLi2SO4
40.25 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorDetector: CCD / Date: Nov 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 114743 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 10.7
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. measured all: 374203
Reflection shell
*PLUS
Lowest resolution: 1.76 Å / % possible obs: 89.7 % / Num. unique obs: 10457 / Num. measured obs: 27598

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E15

1e15


Resolution: 1.7→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2486753.93 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1159 1 %RANDOM
Rwork0.17 ---
obs0.17 114670 96.6 %-
Displacement parametersBiso mean: 27.76 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2--4.3 Å20 Å2
3----7.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7803 0 252 1416 9471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.6
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_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2.1
X-RAY DIFFRACTIONc_scangle_it2.9
LS refinement shellResolution: 1.7→1.77 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.259 115 1 %
Rwork0.26 9736 -
obs--83.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CI4.PARAMCI4.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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