[English] 日本語
Yorodumi
- PDB-4d3z: The structure of inactive prolegumain from chinese hamster, trigo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d3z
TitleThe structure of inactive prolegumain from chinese hamster, trigonal space group.
ComponentsPROLEGUMAIN
KeywordsHYDROLASE / LEGUMAIN / CYSTEINE PROTEASE / SUCCINIMIDE / ASPARAGINYL ENDOPEPTIDASE / CHO
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / legumain / renal system process / receptor catabolic process / self proteolysis / positive regulation of endothelial cell chemotaxis / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / negative regulation of multicellular organism growth ...negative regulation of ERBB signaling pathway / legumain / renal system process / receptor catabolic process / self proteolysis / positive regulation of endothelial cell chemotaxis / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / proteolysis involved in protein catabolic process / lysosomal lumen / positive regulation of mitotic cell cycle / positive regulation of long-term synaptic potentiation / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / negative regulation of neuron apoptotic process / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / extracellular region
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #130 / : / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold ...Topoisomerase I; Chain A, domain 4 - #130 / : / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCRICETULUS GRISEUS (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, W. / Heinz, D.W. / Krausze, J.
CitationJournal: To be Published
Title: A Detailed Look Into Chinese Hamster Legumain Active Site Structure and Exploration of its Function
Authors: Li, W. / Damme, M. / Buessow, K. / Grimm, I. / Van Den Heuvel, J. / Heinz, D.W. / Krausze, J.
History
DepositionOct 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROLEGUMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2894
Polymers46,6261
Non-polymers6643
Water77543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.810, 50.810, 253.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein PROLEGUMAIN


Mass: 46625.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CRICETULUS GRISEUS (Chinese hamster) / Cell line: LEC3.8.2.1 / Organ: OVARY / References: UniProt: G3I1H5, legumain
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE
Crystal growpH: 8
Details: 0.03 M MGCL2, 0.03 M CACL2, 10%(W/V) PEG 20000, 20%(V/V) PEG 550 MME, 0.1 MOPS/HEPES PH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033191
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033191 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 17828 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 19.3 % / Biso Wilson estimate: 40.26 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 18.1 % / Rmerge(I) obs: 1.269 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FGU

4fgu


Resolution: 2.3→19.824 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 891 5 %
Rwork0.163 --
obs0.1666 17820 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 42 43 3217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083266
X-RAY DIFFRACTIONf_angle_d1.144436
X-RAY DIFFRACTIONf_dihedral_angle_d13.9621187
X-RAY DIFFRACTIONf_chiral_restr0.042486
X-RAY DIFFRACTIONf_plane_restr0.006565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.44420.32831450.23292761X-RAY DIFFRACTION100
2.4442-2.63260.28231430.20642732X-RAY DIFFRACTION100
2.6326-2.89670.29891460.20112765X-RAY DIFFRACTION100
2.8967-3.31420.24451480.18172801X-RAY DIFFRACTION100
3.3142-4.16920.23721500.14392863X-RAY DIFFRACTION100
4.1692-19.82470.17931590.1373007X-RAY DIFFRACTION100
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)
11.6879-0.04350.18220.5858-0.00353.27740.01640.037-0.00590.18760.0308-0.09290.1505-0.0211-0.04160.39450.1231-0.03490.2723-0.02940.2984-4.66063.222818.2329
23.31920.10650.18180.65420.79073.3989-0.02490.0210.24270.00440.1112-0.18280.0240.4582-0.09820.35210.0637-0.00950.2859-0.00580.28615.448313.217716.7903
30.76480.8205-1.02632.4933-2.55063.131-0.294-0.03530.5502-0.3211-0.27930.2108-0.2344-0.37990.32270.5970.3315-0.10870.571-0.17160.5071-26.686923.04927.0077
43.4167-0.1726-0.07293.61151.44434.1571-0.1013-0.74420.21540.3099-0.16110.063-0.1078-0.15850.22460.48180.1351-0.05030.517-0.08330.2988-21.630414.604535.2681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 31 THROUGH 236 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 237 THROUGH 338 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 339 THROUGH 362 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 363 THROUGH 436 )

+
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