[English] 日本語
Yorodumi
- PDB-2xvp: ChiA1 from Aspergillus fumigatus, apostructure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xvp
TitleChiA1 from Aspergillus fumigatus, apostructure
ComponentsCLASS III CHITINASE CHIA1
KeywordsHYDROLASE / GH18 / TIM BARREL / ASPERGILLOSIS
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / side of membrane / extracellular region / plasma membrane
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / chitinase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchuettelkopf, A.W. / van Aalten, D.M.F.
CitationJournal: Chem.Biol. / Year: 2010
Title: Natural Product-Guided Discovery of a Fungal Chitinase Inhibitor.
Authors: Rush, C.L. / Schuettelkopf, A.W. / Hurtado-Guerrero, R. / Blair, D.E. / Ibrahim, A.F.M. / Desvergnes, S. / Eggleston, I.M. / Van Aalten, D.M.F.
History
DepositionOct 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...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 / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CLASS III CHITINASE CHIA1
B: CLASS III CHITINASE CHIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,12412
Polymers68,1742
Non-polymers95010
Water10,863603
1
A: CLASS III CHITINASE CHIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6577
Polymers34,0871
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CLASS III CHITINASE CHIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4675
Polymers34,0871
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.729, 126.077, 213.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1338-

PO4

21A-2014-

HOH

31A-2076-

HOH

41B-2030-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.957354, -0.256074, 0.13379), (-0.056464, 0.619973, 0.782589), (-0.283347, 0.74166, -0.607993)
Vector: 29.965, -16.039, 123.981)

-
Components

#1: Protein CLASS III CHITINASE CHIA1


Mass: 34086.906 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: A1163 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: B0Y2Y2, chitinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPO4 A 1338 IS ON A SPECIAL POSITION (SEE REMARK 375) AND HAS BEEN BUILT WITH ATOMS OMITTED (SEE ...PO4 A 1338 IS ON A SPECIAL POSITION (SEE REMARK 375) AND HAS BEEN BUILT WITH ATOMS OMITTED (SEE REMARK 610). COMPLETE SET OF ATOMS IS SYMMETRY-GENERATED (SEE ALSO REMARK 500 SUBTOPIC: CLOSE CONTACTS).
Sequence detailsEXPRESSED CONSTRUCT INCLUDES RESIDUES 29 TO 337 ONLY. PHE28 OF CHAIN A IS GENERATED BY THE CLONING ...EXPRESSED CONSTRUCT INCLUDES RESIDUES 29 TO 337 ONLY. PHE28 OF CHAIN A IS GENERATED BY THE CLONING SITE PRECEDING THE INSERT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growDetails: 0.42M-0.58M NAH2PO4, 0.83M-0.74M K2HPO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 69723 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UY2

2uy2


Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.162 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24174 3507 5.1 %RANDOM
Rwork0.20155 ---
obs0.20356 65776 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.411 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--2.01 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 48 603 5467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9386867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38725.062243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23215709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4061510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213966
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7431.53087
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32124957
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.08631937
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2314.51908
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 244 -
Rwork0.212 4500 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 19.3495 Å / Origin y: 26.1119 Å / Origin z: 76.0956 Å
111213212223313233
T0.0094 Å2-0.0022 Å20.0042 Å2-0.0323 Å2-0.004 Å2--0.0047 Å2
L0.4318 °20.0242 °2-0.0148 °2-0.9443 °20.2773 °2--0.2787 °2
S-0.0071 Å °0.0272 Å °-0.0302 Å °0.031 Å °-0.0155 Å °0.0222 Å °0.0121 Å °-0.0089 Å °0.0226 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 337
2X-RAY DIFFRACTION1B28 - 337
3X-RAY DIFFRACTION1A2001 - 2316
4X-RAY DIFFRACTION1B2001 - 2287
5X-RAY DIFFRACTION1A1338 - 1343
6X-RAY DIFFRACTION1B - A1338 - 1343

+
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