[English] 日本語
Yorodumi
- PDB-4rtd: Escherichia coli alpha-2-macroglobulin activated by porcine elastase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rtd
TitleEscherichia coli alpha-2-macroglobulin activated by porcine elastase
ComponentsUncharacterized lipoprotein YfhM
KeywordsLIPID BINDING PROTEIN / thioester domain / macroglobulin
Function / homology
Function and homology information


endopeptidase inhibitor activity / defense response / protein homodimerization activity / extracellular space / plasma membrane
Similarity search - Function
Alpha-2-macroglobulin MG3 domain / Alpha-2-macroglobulin, bacteria / Alpha-2-macroglobulin, MG1 domain / Bacterial Alpha-2-macroglobulin, MG5 domain / Bacterial alpha-2-macroglobulin MG10 domain / Bacterial Alpha-2-macroglobulin, MG6 domain / : / : / : / Bacterial alpha-2-macroglobulin MG3 domain ...Alpha-2-macroglobulin MG3 domain / Alpha-2-macroglobulin, bacteria / Alpha-2-macroglobulin, MG1 domain / Bacterial Alpha-2-macroglobulin, MG5 domain / Bacterial alpha-2-macroglobulin MG10 domain / Bacterial Alpha-2-macroglobulin, MG6 domain / : / : / : / Bacterial alpha-2-macroglobulin MG3 domain / Bacterial macroglobulin domain 6 / Bacterial Alpha-2-macroglobulin MG1 domain / Bacterial Alpha-2-macroglobulin MG5 domain / Bacterial Alpha-2-macroglobulin MG10 domain / Bacterial alpha-2 macroglobulin MG2 domain / A2MG, CUB domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Alpha-2-macroglobulin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.65 Å
AuthorsFyfe, C.D. / Grinter, R. / Roszak, A.W. / Josts, I. / Cogdell, R.J. / Walker, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of protease-cleaved Escherichia coli alpha-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment.
Authors: Fyfe, C.D. / Grinter, R. / Josts, I. / Mosbahi, K. / Roszak, A.W. / Cogdell, R.J. / Wall, D.M. / Burchmore, R.J. / Byron, O. / Walker, D.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized lipoprotein YfhM


Theoretical massNumber of molelcules
Total (without water)181,6181
Polymers181,6181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.065, 176.065, 161.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Uncharacterized lipoprotein YfhM


Mass: 181618.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2520, JW2504, yfhM / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76578
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M potassium chloride, 25% SOKALAN CP7, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.65→46.87 Å / Num. all: 20753 / Num. obs: 20753 / % possible obs: 99.9 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 26.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.2
Reflection shellResolution: 3.65→4 Å / Redundancy: 26.7 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
EDNAdata collection
AutoSolphasing
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.65→46.87 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 76.202 / SU ML: 0.491 / Cross valid method: THROUGHOUT / ESU R Free: 0.588 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23831 1033 5 %RANDOM
Rwork0.17746 ---
all0.18042 20753 --
obs0.18042 19679 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 3.65→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 0 0 8699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198882
X-RAY DIFFRACTIONr_bond_other_d0.0020.028449
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.97512081
X-RAY DIFFRACTIONr_angle_other_deg0.834319429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47551117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8524.903414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.308151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8811557
X-RAY DIFFRACTIONr_chiral_restr0.0750.21340
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021991
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_it6.5111.2914483
X-RAY DIFFRACTIONr_mcbond_other6.50811.2924482
X-RAY DIFFRACTIONr_mcangle_it10.55216.9275595
X-RAY DIFFRACTIONr_mcangle_other10.55116.9275596
X-RAY DIFFRACTIONr_scbond_it6.23711.7554399
X-RAY DIFFRACTIONr_scbond_other6.23611.7544400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1917.4626487
X-RAY DIFFRACTIONr_long_range_B_refined15.88992.52210186
X-RAY DIFFRACTIONr_long_range_B_other15.88892.52110187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.65→3.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 73 -
Rwork0.311 1462 -
obs--99.48 %
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)
11.80020.3070.20461.9879-0.22670.10270.0268-0.3910.04340.2979-0.1047-0.33150.0508-0.08650.07790.2358-0.03080.02040.3827-0.0210.087-46.647334.2593-18.8426
24.4261-1.8128-1.15692.56140.88581.0922-0.0577-0.3034-0.5074-0.00460.2075-0.0550.23630.3302-0.14980.46360.0111-0.03390.34190.09230.2591-45.2246-3.2228-28.3827
31.83050.1571-0.46831.7705-0.77930.89880.05670.0402-0.1042-0.2949-0.07420.24550.1612-0.17030.01750.1727-0.0620.01070.1372-0.07350.0813-66.865129.179-41.9534
42.5169-1.5513-0.69281.4903-0.06953.87920.00260.0873-0.23790.1323-0.11470.46910.144-0.30590.1120.0826-0.05630.07830.0617-0.03120.3837-34.930735.1078-83.4727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A379 - 485
2X-RAY DIFFRACTION1A853 - 922
3X-RAY DIFFRACTION1A943 - 1019
4X-RAY DIFFRACTION2A486 - 610
5X-RAY DIFFRACTION2A611 - 622
6X-RAY DIFFRACTION2A637 - 677
7X-RAY DIFFRACTION2A691 - 743
8X-RAY DIFFRACTION3A1020 - 1127
9X-RAY DIFFRACTION3A1128 - 1168
10X-RAY DIFFRACTION3A1440 - 1498
11X-RAY DIFFRACTION3A1499 - 1560
12X-RAY DIFFRACTION3A1566 - 1653
13X-RAY DIFFRACTION4A1169 - 1439

+
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