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- PDB-7fbt: Crystal structure of chitinase (RmChi1) from Rhizomucor miehei (s... -

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Basic information

Entry
Database: PDB / ID: 7fbt
TitleCrystal structure of chitinase (RmChi1) from Rhizomucor miehei (sp p32 2 1, MR)
ComponentsChitinase
KeywordsHYDROLASE / Fungal chitinase / Rhizomucor miehei / P32 2 1
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region / metal ion binding
Similarity search - Function
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Fungal chitinase from Rhizomucor miehei (Native protein)
Similarity search - Component
Biological speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiang, Z.Q. / Hu, S.Q. / Zhu, Q. / Liu, Y.C. / Ma, J.W. / Yan, Q.J. / Gao, Y.G. / Yang, S.Q.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2021
Title: Crystal structure of a chitinase (RmChiA) from the thermophilic fungus Rhizomucor miehei with a real active site tunnel.
Authors: Jiang, Z. / Hu, S. / Ma, J. / Liu, Y. / Qiao, Z. / Yan, Q. / Gao, Y. / Yang, S.
History
DepositionJul 12, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 11, 2021ID: 5XWQ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5103
Polymers41,4621
Non-polymers492
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-13 kcal/mol
Surface area13420 Å2
Unit cell
Length a, b, c (Å)45.384, 45.384, 250.522
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein Chitinase


Mass: 41461.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UEQ2, chitinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.81 Å3/Da / Density % sol: 31.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM MgCl2, 30 % (w/v) PEG 4000, 100 mM Tris-Cl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9643 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9643 Å / Relative weight: 1
ReflectionResolution: 1.9→33.29 Å / Num. obs: 23722 / % possible obs: 95.6 % / Redundancy: 27.82 % / Biso Wilson estimate: 32.88 Å2 / CC1/2: 1 / Rrim(I) all: 0.08 / Net I/σ(I): 30.94
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 11.66 % / Mean I/σ(I) obs: 3.46 / Num. unique obs: 3113 / CC1/2: 0.85 / Rrim(I) all: 0.75 / % possible all: 80.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITX

1itx


Resolution: 1.9→33.29 Å / SU ML: 0.2762 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.8514
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.296 2372 10 %
Rwork0.2729 21348 -
obs0.2751 23720 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 2 179 2595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632478
X-RAY DIFFRACTIONf_angle_d0.9453375
X-RAY DIFFRACTIONf_chiral_restr0.0591377
X-RAY DIFFRACTIONf_plane_restr0.005437
X-RAY DIFFRACTIONf_dihedral_angle_d16.7562869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.41681050.3729937X-RAY DIFFRACTION75.13
1.94-1.980.34451190.34111070X-RAY DIFFRACTION81.61
1.98-2.030.32951180.32691063X-RAY DIFFRACTION85.09
2.03-2.080.32011310.32931181X-RAY DIFFRACTION90.11
2.08-2.130.34641320.33861187X-RAY DIFFRACTION94.35
2.13-2.20.35961420.31171281X-RAY DIFFRACTION97.94
2.2-2.270.32221440.30951300X-RAY DIFFRACTION100
2.27-2.350.32071420.30391274X-RAY DIFFRACTION100
2.35-2.440.31211450.30461302X-RAY DIFFRACTION100
2.44-2.550.36321440.31771302X-RAY DIFFRACTION100
2.55-2.690.33261460.31310X-RAY DIFFRACTION100
2.69-2.860.33191460.29791316X-RAY DIFFRACTION100
2.86-3.080.30621460.26241313X-RAY DIFFRACTION100
3.08-3.390.29151460.2661316X-RAY DIFFRACTION100
3.39-3.880.28461510.23581355X-RAY DIFFRACTION100
3.88-4.880.24691510.22321365X-RAY DIFFRACTION99.93
4.89-33.290.26731640.27181476X-RAY DIFFRACTION99.7

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