[English] 日本語
Yorodumi
- PDB-2x3a: AsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x3a
TitleAsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloendopeptidase
ComponentsTOXIC EXTRACELLULAR ENDOPEPTIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


metalloendopeptidase activity / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2970 / Lysine-specific metallo-endopeptidase / Peptidyl-Lys metallopeptidase catalytic domain / Lysine-specific metallo-endopeptidase / Lysine-specific metallo-endopeptidase / : / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Immunoglobulin-like ...Immunoglobulin-like - #2970 / Lysine-specific metallo-endopeptidase / Peptidyl-Lys metallopeptidase catalytic domain / Lysine-specific metallo-endopeptidase / Lysine-specific metallo-endopeptidase / : / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Toxic extracellular endopeptidase
Similarity search - Component
Biological speciesAEROMONAS SALMONICIDA SUBSP. ACHROMOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBogdanovic, X. / Palm, G.J. / Singh, R.K. / Hinrichs, W.
Citation
Journal: FEBS Lett. / Year: 2016
Title: Structural Evidence of Intramolecular Propeptide Inhibition of the Aspzincin Metalloendopeptidase Asap1.
Authors: Bogdanovic, X. / Palm, G.J. / Schwenteit, J. / Singh, R.K. / Gudmundsdottir, B.K. / Hinrichs, W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Asap1_E294A and Asap1_E294Q, Two Inactive Mutants of the Toxic Zinc Metallopeptidase Asap1 from Aeromonas Salmonicida Subsp. Achromogenes.
Authors: Bogdanovic, X. / Singh, R.K. / Hentschke, J. / Gudmundsdottir, B.K. / Hinrichs, W.
#2: Journal: J.Bacteriol. / Year: 2009
Title: The Asap1 Peptidase of Aeromonas Salmonicida Subsp. Achromogenes is a Highly Conserved Deuterolysin Metalloprotease (Family M35) and a Major Virulence Factor.
Authors: Arnadottir, H. / Hvanndal, I. / Andresdottir, V. / Burr, S.E. / Frey, J. / Gudmundsdottir, B.K.
#3: Journal: Dis.Aquat.Organ. / Year: 1990
Title: Isolation of a New Toxic Protease from a Strain of Aeromonas Salmonicida Subspecies Achromogenes
Authors: Gudmundsdottir, B.K. / Hastingst, S. / Ellis, E.A.
History
DepositionJan 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Oct 12, 2016Group: Database references
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0198
Polymers37,2861
Non-polymers7337
Water3,585199
1
A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules

A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,03716
Polymers74,5712
Non-polymers1,46614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5480 Å2
ΔGint-152.6 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.249, 74.468, 54.703
Angle α, β, γ (deg.)90.00, 112.35, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein TOXIC EXTRACELLULAR ENDOPEPTIDASE


Mass: 37285.539 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEROMONAS SALMONICIDA SUBSP. ACHROMOGENES (bacteria)
Strain: KELDUR265-87 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PRI3715 / References: UniProt: Q8GMV9, deuterolysin

-
Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 294 TO GLN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2 M MES PH 7.5, 1.6 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.95369
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. obs: 24682 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.17
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / % possible all: 86.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X3C

2x3c


Resolution: 2→57.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.686 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20461 1258 5.1 %RANDOM
Rwork0.17014 ---
obs0.17203 23411 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å22.82 Å2
2---0.43 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→57.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 40 199 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222370
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9593227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02924.732112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66215362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9871513
X-RAY DIFFRACTIONr_chiral_restr0.1490.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211819
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_it1.1041.51474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85622361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1953896
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7824.5865
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: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 73 -
Rwork0.272 1632 -
obs--93.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32791.2519-0.10281.8945-0.35020.1005-0.0268-0.035-0.04640.04680.0005-0.0871-0.0093-0.02220.02620.0914-0.06120.01820.0671-0.04040.047715.8155.728930.2605
21.74551.1725-0.50030.7913-0.36270.6832-0.08520.1689-0.1559-0.04510.1228-0.10190.0658-0.2285-0.03760.0776-0.0105-0.00430.0790.01010.027118.386662.153224.7162
31.85551.4275-0.53382.06490.81882.48370.067-0.0248-0.04810.0579-0.04730.06860.0377-0.1437-0.01970.0756-0.0125-0.01530.0709-0.00360.063216.646366.461336.0543
41.6017-0.0855-0.09821.07150.08861.1159-0.04070.1333-0.0204-0.0960.03560.1567-0.0861-0.11550.00510.06190.0017-0.02540.03060.00670.026629.85174.97710.5118
58.0463-1.9723-1.65673.2137-1.0712.7786-0.21550.2542-0.7202-0.13870.0530.70150.3279-0.43590.16250.1197-0.0594-0.04590.1348-0.02260.280916.743671.12999.6438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 64
2X-RAY DIFFRACTION2A65 - 103
3X-RAY DIFFRACTION3A104 - 155
4X-RAY DIFFRACTION4A175 - 304
5X-RAY DIFFRACTION5A305 - 340

+
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