[English] 日本語
Yorodumi
- PDB-6zep: Flavourzyme Leucine Aminopeptidase A proenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zep
TitleFlavourzyme Leucine Aminopeptidase A proenzyme
ComponentsLeucine aminopeptidase A
KeywordsHYDROLASE / M28 peptidase / prodomain / intramolecular chaperone / bimetallic aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28 family / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Leucine aminopeptidase A
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsWatson, K.A. / Baltulionis, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K012053/1 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2021
Title: The role of propeptide-mediated autoinhibition and intermolecular chaperone in the maturation of cognate catalytic domain in leucine aminopeptidase.
Authors: Baltulionis, G. / Blight, M. / Robin, A. / Charalampopoulos, D. / Watson, K.A.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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: Leucine aminopeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7776
Polymers41,1521
Non-polymers1,6265
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-67 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.430, 94.390, 99.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Leucine aminopeptidase A / Leucyl aminopeptidase A / LAPA


Mass: 41151.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (strain ATCC 42149 / RIB 40) (mold)
Gene: lapA, AO090011000052 / Production host: Komagataella pastoris (fungus) / Variant (production host): X33
References: UniProt: Q2U1F3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 486 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris, pH = 5.5, 0.2 M NaCl, 25% PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.61→42.611 Å / Num. obs: 53338 / % possible obs: 99.48 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.07303 / Net I/σ(I): 11.36
Reflection shellResolution: 1.61→1.668 Å / Rmerge(I) obs: 0.8915 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 5269 / CC1/2: 0.55 / CC star: 0.842 / Rrim(I) all: 0.08292

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTQ

1rtq


Resolution: 1.61→42.611 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.16
RfactorNum. reflection% reflection
Rfree0.1739 2671 5.01 %
Rwork0.1527 --
obs0.1537 53338 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.61→42.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 101 482 3201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072869
X-RAY DIFFRACTIONf_angle_d0.933910
X-RAY DIFFRACTIONf_dihedral_angle_d15.0091726
X-RAY DIFFRACTIONf_chiral_restr0.057450
X-RAY DIFFRACTIONf_plane_restr0.006502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.63930.31311390.3042604X-RAY DIFFRACTION100
1.6393-1.67080.27711460.27652666X-RAY DIFFRACTION100
1.6708-1.70490.29451470.26242591X-RAY DIFFRACTION100
1.7049-1.7420.26911710.23022618X-RAY DIFFRACTION100
1.742-1.78250.23311630.21722609X-RAY DIFFRACTION100
1.7825-1.82710.20441310.19612656X-RAY DIFFRACTION100
1.8271-1.87650.22541370.18482643X-RAY DIFFRACTION100
1.8765-1.93170.20351300.18442651X-RAY DIFFRACTION100
1.9317-1.99410.21611270.17662678X-RAY DIFFRACTION100
1.9941-2.06530.19791170.16962634X-RAY DIFFRACTION98
2.0653-2.1480.20611390.15182667X-RAY DIFFRACTION100
2.148-2.24580.17881430.1472666X-RAY DIFFRACTION100
2.2458-2.36420.17311210.14142696X-RAY DIFFRACTION100
2.3642-2.51230.17631130.14372686X-RAY DIFFRACTION100
2.5123-2.70620.16181580.14132657X-RAY DIFFRACTION99
2.7062-2.97850.18121240.14512705X-RAY DIFFRACTION100
2.9785-3.40930.16961480.13472698X-RAY DIFFRACTION100
3.4093-4.29470.12311610.11822699X-RAY DIFFRACTION98
4.2947-42.6110.13611560.13512843X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.4382 Å / Origin y: -2.2698 Å / Origin z: 9.909 Å
111213212223313233
T0.1076 Å2-0.0002 Å2-0.0007 Å2-0.1126 Å20.0089 Å2--0.1336 Å2
L0.975 °20.2036 °20.1458 °2-0.8144 °20.2231 °2--1.3686 °2
S-0.0181 Å °0.0085 Å °0.0229 Å °0.0202 Å °0.003 Å °0.0355 Å °-0.014 Å °-0.0538 Å °0.0091 Å °
Refinement TLS groupSelection details: all

+
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