[English] 日本語
Yorodumi
- PDB-9i2p: Crystal structure of Listeria monocytogenes ChiA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i2p
TitleCrystal structure of Listeria monocytogenes ChiA
Componentschitinase
KeywordsHYDROLASE / chitinase / Listeria monocytogenes / ChiA / GH18
Function / homology
Function and homology information


chitinase / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / 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
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRehman, S. / Garnett, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R017662/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure and analysis of Listeria monocytogenes ChiA
Authors: Rehman, S. / Garnett, J.A.
History
DepositionJan 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 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)70,8608
Polymers70,4472
Non-polymers4136
Water7,206400
1
A: chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4015
Polymers35,2231
Non-polymers1784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4593
Polymers35,2231
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.041, 59.146, 67.609
Angle α, β, γ (deg.)94.308, 110.69, 111.596
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 323 / Label seq-ID: 1 - 323

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein chitinase


Mass: 35223.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: lmo1883 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y619, chitinase

-
Non-polymers , 5 types, 406 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% (w/v) PEG 4000, 20% (w/v) glycerol, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM (RS)-1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol, 100 mM 2-(N- ...Details: 10% (w/v) PEG 4000, 20% (w/v) glycerol, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM (RS)-1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol, 100 mM 2-(N-morpholino) ethane sulfonic acid (MES), 100 mM imidazole

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.95→45.67 Å / Num. obs: 48104 / % possible obs: 93 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.344 / Num. unique obs: 3600 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→45.592 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2256 2399 4.985 %
Rwork0.1798 45726 -
all0.182 --
obs-48104 92.864 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.532 Å2
Baniso -1Baniso -2Baniso -3
1-2.288 Å20.911 Å2-0.467 Å2
2--1.97 Å2-0.83 Å2
3----2.881 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 22 400 5400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125115
X-RAY DIFFRACTIONr_bond_other_d00.0164734
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.7856955
X-RAY DIFFRACTIONr_angle_other_deg0.6011.75610912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.409512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74510800
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.82210234
X-RAY DIFFRACTIONr_chiral_restr0.0890.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026080
X-RAY DIFFRACTIONr_gen_planes_other0.0230.021168
X-RAY DIFFRACTIONr_nbd_refined0.220.21011
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.24304
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22637
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2317
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.29
X-RAY DIFFRACTIONr_nbd_other0.1880.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.25
X-RAY DIFFRACTIONr_mcbond_it3.6421.4812582
X-RAY DIFFRACTIONr_mcbond_other3.6341.482582
X-RAY DIFFRACTIONr_mcangle_it4.712.6393224
X-RAY DIFFRACTIONr_mcangle_other4.7132.6393225
X-RAY DIFFRACTIONr_scbond_it5.9291.9842533
X-RAY DIFFRACTIONr_scbond_other5.9281.9852534
X-RAY DIFFRACTIONr_scangle_it8.2543.3493731
X-RAY DIFFRACTIONr_scangle_other8.2533.353732
X-RAY DIFFRACTIONr_lrange_it9.67315.9625917
X-RAY DIFFRACTIONr_lrange_other9.67315.6995833
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.0510518
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.081640.05008
12BX-RAY DIFFRACTIONLocal ncs0.081640.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.9980.2971650.2693337X-RAY DIFFRACTION91.0083
1.998-2.0520.2991590.2613253X-RAY DIFFRACTION91.0109
2.052-2.1120.2861680.233159X-RAY DIFFRACTION92.0332
2.112-2.1760.2471600.2123091X-RAY DIFFRACTION92.4105
2.176-2.2480.2391550.2133062X-RAY DIFFRACTION94.8688
2.248-2.3260.2461540.1882846X-RAY DIFFRACTION90.6071
2.326-2.4140.2611470.1862735X-RAY DIFFRACTION90.8862
2.414-2.5120.2331360.1712707X-RAY DIFFRACTION92.0661
2.512-2.6230.2281350.1712568X-RAY DIFFRACTION91.8139
2.623-2.7510.281390.1772467X-RAY DIFFRACTION92.3458
2.751-2.8990.2081110.1562362X-RAY DIFFRACTION93.1099
2.899-3.0740.191310.1512221X-RAY DIFFRACTION92.562
3.074-3.2860.231160.1522074X-RAY DIFFRACTION92.6004
3.286-3.5470.203980.1642033X-RAY DIFFRACTION95.0491
3.547-3.8840.201970.1551836X-RAY DIFFRACTION94.3387
3.884-4.3380.196860.1531670X-RAY DIFFRACTION96.7493
4.338-5.0020.171790.1351536X-RAY DIFFRACTION98.4756
5.002-6.1070.199740.1871240X-RAY DIFFRACTION95.1484
6.107-8.5610.182520.175978X-RAY DIFFRACTION96.4419
8.561-45.5920.153370.17551X-RAY DIFFRACTION97.351

+
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