[English] 日本語
Yorodumi
- PDB-9hj7: Structure of Chitinase 35 from Metschnikowia pulcherrima (MpChit35) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hj7
TitleStructure of Chitinase 35 from Metschnikowia pulcherrima (MpChit35)
ComponentsChitinase
KeywordsHYDROLASE / Chitinase / exochitinase
Function / homology
Function and homology information


endochitinase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chitinase
Similarity search - Component
Biological speciesMetschnikowia pulcherrima (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFernandez-Garcia, A. / Sanz-Aparicio, J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105838RB-C33 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-136367OB-C33 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural-mechanistic insights and performance engineering of chitinase MpChit35 for tailored chito-oligosaccharide production.
Authors: Minguet-Lobato, M. / Fernandez-Garcia, A. / Jimenez-Ortega, E. / Cervantes, F.V. / Sanchez-Pozo, P. / Plou, F.J. / Sanz-Aparicio, J. / Fernandez-Lobato, M.
History
DepositionNov 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,39013
Polymers64,1802
Non-polymers1,21011
Water2,720151
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5686
Polymers32,0901
Non-polymers4785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8227
Polymers32,0901
Non-polymers7326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.582, 54.850, 97.776
Angle α, β, γ (deg.)90.00, 107.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Chitinase


Mass: 32089.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metschnikowia pulcherrima (fungus) / Gene: MPUL0D06620, METSCH_D06620 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: A0A4P6XUI5
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 161 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 4000, 100mM magnesium chloride, 100mM sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2023 / Details: KB MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→47.31 Å / Num. obs: 20240 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.08 / Rrim(I) all: 0.201 / Χ2: 1.42 / Net I/σ(I): 7.5
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2416 / CC1/2: 0.915 / Rpim(I) all: 0.213 / Rrim(I) all: 0.521 / Χ2: 1.94 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→47.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.904 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 3.998 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23817 976 4.9 %RANDOM
Rwork0.18108 ---
obs0.18386 19134 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0 Å2-2.04 Å2
2--0.03 Å2-0 Å2
3---2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.55→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 29 151 4740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164248
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.7966413
X-RAY DIFFRACTIONr_angle_other_deg0.491.7499799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.735520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00910716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021135
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_it1.7532.3762338
X-RAY DIFFRACTIONr_mcbond_other1.7472.3762338
X-RAY DIFFRACTIONr_mcangle_it2.8554.2622922
X-RAY DIFFRACTIONr_mcangle_other2.8544.2652923
X-RAY DIFFRACTIONr_scbond_it2.5422.7382392
X-RAY DIFFRACTIONr_scbond_other2.5412.7392393
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1354.863486
X-RAY DIFFRACTIONr_long_range_B_refined6.78524.495271
X-RAY DIFFRACTIONr_long_range_B_other6.78424.55272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.611 Å
RfactorNum. reflection% reflection
Rfree0.244 63 -
Rwork0.272 1365 -
obs--94.07 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more