[English] 日本語
Yorodumi
- PDB-6udg: Crystal structure of a Probable thiol peroxidase from Elizabethki... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6udg
TitleCrystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Elizabethkingia anophelis / tpx / Thiol peroxidase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiol peroxidase
B: Thiol peroxidase
C: Thiol peroxidase
D: Thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)74,3714
Polymers74,3714
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-31 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.590, 107.800, 113.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 or (resid 6 through 7...
21(chain B and (resid 5 through 13 or (resid 14...
31(chain C and (resid 5 through 13 or (resid 14...
41(chain D and (resid 5 through 8 or (resid 9...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain A and (resid 5 or (resid 6 through 7...AA513
12LEULEULYSLYS(chain A and (resid 5 or (resid 6 through 7...AA6 - 714 - 15
13ASNASNLYSLYS(chain A and (resid 5 or (resid 6 through 7...AA3 - 16511 - 173
14ASNASNLYSLYS(chain A and (resid 5 or (resid 6 through 7...AA3 - 16511 - 173
15ASNASNLYSLYS(chain A and (resid 5 or (resid 6 through 7...AA3 - 16511 - 173
21THRTHRTHRTHR(chain B and (resid 5 through 13 or (resid 14...BB5 - 1313 - 21
22VALVALVALVAL(chain B and (resid 5 through 13 or (resid 14...BB1422
23THRTHRLYSLYS(chain B and (resid 5 through 13 or (resid 14...BB5 - 16513 - 173
31THRTHRTHRTHR(chain C and (resid 5 through 13 or (resid 14...CC5 - 1313 - 21
32VALVALVALVAL(chain C and (resid 5 through 13 or (resid 14...CC1422
33ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
34ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
35ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
36ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
41THRTHRGLYGLY(chain D and (resid 5 through 8 or (resid 9...DD5 - 813 - 16
42ASNASNILEILE(chain D and (resid 5 through 8 or (resid 9...DD9 - 1117 - 19
43ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173
44ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173
45ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173
46ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173

-
Components

#1: Protein
Thiol peroxidase / Tpx / Peroxiredoxin tpx / Prx / Thioredoxin peroxidase


Mass: 18592.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: tpx, BD94_2659 / Plasmid: ElanA.00055.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A077EJK0, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Anatrace Morpheus screen, well g8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium Ltartrate, sodium ...Details: Anatrace Morpheus screen, well g8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium Ltartrate, sodium oxamate: 100mM MOPS/HEPES-Na pH 7.5: ElanA.00055.a.B1, PW38308, at 23mg/ml: cryo: direct: tray 294018 g8: puck xoe2-6.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 24, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→48.7 Å / Num. obs: 19753 / % possible obs: 99.7 % / Redundancy: 4.84 % / Biso Wilson estimate: 64.797 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.078 / Χ2: 0.991 / Net I/σ(I): 14.18 / Num. measured all: 95601 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.724.9830.6182.847131143414310.8820.69399.8
2.72-2.794.9830.5013.397056141714160.9080.56299.9
2.79-2.874.9790.4523.746682134313420.9180.50799.9
2.87-2.964.9680.3364.966632133713350.9620.37799.9
2.96-3.064.9380.2576.026330128512820.9740.28999.8
3.06-3.174.9540.1987.486262126712640.9830.22299.8
3.17-3.294.910.1668.435809118311830.9860.187100
3.29-3.424.9130.12810.755674115611550.9920.14399.9
3.42-3.574.9130.09213.75596114011390.9960.10399.9
3.57-3.754.8680.07316.75121105510520.9970.08299.7
3.75-3.954.820.06518.564940102510250.9970.073100
3.95-4.194.7910.05620.7946289689660.9970.06399.8
4.19-4.484.7260.04723.7443869349280.9980.05299.4
4.48-4.844.7560.04427.1840098478430.9980.04999.5
4.84-5.34.7080.04127.9336637817780.9970.04699.6
5.3-5.934.6920.04427.4934257327300.9980.04999.7
5.93-6.844.5660.04129.2929046396360.9980.04699.5
6.84-8.384.4850.03532.2824715545510.9980.0499.5
8.38-11.854.2890.03536.0118834434390.9980.03999.1
11.85-48.73.8720.03433.989992702580.9990.03895.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4je1A

Resolution: 2.65→48.7 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.8
RfactorNum. reflection% reflection
Rfree0.2805 2096 10.63 %
Rwork0.2095 --
obs0.2171 19723 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.73 Å2 / Biso mean: 80.7365 Å2 / Biso min: 38.83 Å2
Refinement stepCycle: final / Resolution: 2.65→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 0 11 4557
Biso mean---56.5 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044612
X-RAY DIFFRACTIONf_angle_d0.7336327
X-RAY DIFFRACTIONf_dihedral_angle_d13.4492738
X-RAY DIFFRACTIONf_chiral_restr0.048775
X-RAY DIFFRACTIONf_plane_restr0.006859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2619X-RAY DIFFRACTION12.011TORSIONAL
12B2619X-RAY DIFFRACTION12.011TORSIONAL
13C2619X-RAY DIFFRACTION12.011TORSIONAL
14D2619X-RAY DIFFRACTION12.011TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.710.40761510.35411511302100
2.71-2.780.43651460.326211201266100
2.78-2.850.42751500.314211651315100
2.85-2.940.38311180.291411611279100
2.94-3.030.41151400.28551151129199
3.03-3.140.41831350.270311671302100
3.14-3.270.31991390.265111541293100
3.27-3.420.33191020.24212031305100
3.42-3.60.30631320.208311931325100
3.6-3.820.25681550.20111531308100
3.82-4.120.32761160.195612001316100
4.12-4.530.22531700.1681142131299
4.53-5.190.23661380.160811971335100
5.19-6.530.22851560.209411971353100
6.53-48.70.22531480.16861273142198
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)
14.5441-1.58210.14033.06870.99354.0256-0.1512-0.16690.44890.06860.11450.2444-0.1719-0.23160.0720.38850.01410.05150.43630.02980.7449-15.23669.1545-27.6511
22.77930.41510.35995.9109-0.86585.657-0.1348-0.3619-0.62310.39290.2524-0.02080.18780.0999-0.17080.45820.08850.08260.45490.05240.65559.812428.2507-16.4513
33.47650.4837-0.52063.475-1.83766.263-0.27620.52610.3-0.84530.45180.79970.0387-0.3571-0.17480.6632-0.143-0.11830.54990.13120.76095.989936.3675-45.6495
45.3304-1.8524-0.79331.92270.6431.43320.10260.3425-0.0864-0.38080.0801-0.69690.00630.2465-0.2080.5277-0.0780.15260.5174-0.16320.957310.06760.448-42.8723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 165)A3 - 165
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 165)B5 - 165
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 165)C4 - 165
4X-RAY DIFFRACTION4(chain 'D' and resid 4 through 165)D4 - 165

+
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