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- PDB-4z2k: Serratia marcescens Chitinase B complexed with macrolide inhibitor 32 -

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Basic information

Entry
Database: PDB / ID: 4z2k
TitleSerratia marcescens Chitinase B complexed with macrolide inhibitor 32
ComponentsChitinase B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Chitinase / Inhibitor / Macrolide / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / 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
Chem-M6E / Chitinase B
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaita, N. / Sugawara, A. / Sunazuka, T.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase
Authors: Sugawara, A. / Maita, N. / Gouda, H. / Yamamoto, T. / Hirose, T. / Kimura, S. / Saito, Y. / Nakano, H. / Kasai, T. / Nakano, H. / Shiomi, K. / Hirono, S. / Watanabe, T. / Taniguchi, H. / Omura, S. / Sunazuka, T.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9565
Polymers55,9251
Non-polymers1,0304
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-1 kcal/mol
Surface area20380 Å2
2
A: Chitinase B
hetero molecules

A: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,91110
Polymers111,8512
Non-polymers2,0608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3550 Å2
ΔGint-14 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.740, 97.740, 197.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-658-

HOH

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Components

#1: Protein Chitinase B


Mass: 55925.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiB / Plasmid: pTrcHisB / Production host: Escherichia coli DH5alpha (bacteria) / Strain (production host): DH5alpha / References: UniProt: P11797, chitinase
#2: Chemical ChemComp-M6E / (1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,17S)-3-ethyl-2,10-dihydroxy-2,6,8,10,12,15,15,17-octamethyl-5-oxo-9-(prop-2-yn-1-yloxy)-4,14,16-trioxabicyclo[11.3.1]heptadec-7-yl {7-[N'-(methylcarbamoyl)carbamimidamido]heptyl}carbamate


Mass: 753.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H67N5O10
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 4.21 Å3/Da / Density % sol: 70.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes-Na pH7.0, 0.8M ammonium sulfate, 5% (v/v) glycerol
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 43331 / Num. obs: 43331 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 15.9
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WD0

3wd0


Resolution: 2.3→39.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.847 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19412 2179 5 %RANDOM
Rwork0.16812 ---
obs0.16945 41069 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2--0.04 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.3→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 71 240 4224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024094
X-RAY DIFFRACTIONr_bond_other_d0.0010.023751
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9545580
X-RAY DIFFRACTIONr_angle_other_deg0.738596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61124.124194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69215601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3671520
X-RAY DIFFRACTIONr_chiral_restr0.090.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214725
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021009
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 156 -
Rwork0.21 2976 -
obs--100 %

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