[English] 日本語
Yorodumi
- PDB-5cp1: Crystal structure of C239S mutant of a novel disulfide oxidoreduc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cp1
TitleCrystal structure of C239S mutant of a novel disulfide oxidoreductase from Deinococcus radiodurans
ComponentsFrnE protein
KeywordsOXIDOREDUCTASE / Disulfide isomerase / Disulfide oxidoreductase / FrnE
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FrnE protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsBihani, S.C. / Panicker, L. / Kumar, V.
CitationJournal: To Be Published
Title: Crystal structure of a novel disulfide oxidoreductase from Deinococcus radiodurans
Authors: Bihani, S.C. / Panicker, L. / Kumar, V. / Misra, H.S. / Rajpurohit, Y.S.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FrnE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0268
Polymers28,4781
Non-polymers5497
Water2,918162
1
A: FrnE protein
hetero molecules

A: FrnE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,05316
Polymers56,9562
Non-polymers1,09714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_458-x-1,y,-z+31
Buried area2870 Å2
ΔGint-4 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.091, 66.158, 84.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

-
Components

#1: Protein FrnE protein


Mass: 28477.809 Da / Num. of mol.: 1 / Mutation: C239S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0659 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RWK7
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG 8000, Glycerol, Sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→31.94 Å / Num. obs: 26030 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO3

5co3


Resolution: 1.801→31.935 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 1253 4.82 %
Rwork0.1625 24720 -
obs0.1641 25973 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.68 Å2 / Biso mean: 26.6387 Å2 / Biso min: 9.08 Å2
Refinement stepCycle: final / Resolution: 1.801→31.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 36 162 2066
Biso mean--42.96 35.91 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061943
X-RAY DIFFRACTIONf_angle_d0.9072628
X-RAY DIFFRACTIONf_chiral_restr0.038278
X-RAY DIFFRACTIONf_plane_restr0.004353
X-RAY DIFFRACTIONf_dihedral_angle_d14.399706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8011-1.87320.28661420.243226972839100
1.8732-1.95840.24121470.202627002847100
1.9584-2.06160.21441360.178327042840100
2.0616-2.19080.18131230.158827112834100
2.1908-2.35990.19721450.15127322877100
2.3599-2.59730.20911240.161927472871100
2.5973-2.97280.20261480.158327402888100
2.9728-3.74450.1971260.148328092935100
3.7445-31.93960.16641620.15782880304299
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)
13.36510.1047-0.87121.02210.26222.257-0.0257-0.3726-0.50750.43790.0140.27260.3685-0.07340.03720.3117-0.02310.05480.17070.05760.29751.8134143.5125107.9397
21.48370.15550.19451.1219-0.16960.4841-0.0456-0.1706-0.20540.23320.02190.17010.0354-0.01330.02240.18960.00370.0270.14580.03140.1628-1.9595151.7264104.7833
30.1621-0.12740.21090.2778-0.61151.2634-0.0570.3352-0.1956-0.2184-0.0361-0.18040.28420.30240.05110.21040.01240.04470.3007-0.07110.230619.3236152.980789.0066
41.2170.32230.06890.72010.09810.93760.04960.0719-0.0838-0.04210.0397-0.01190.0315-0.0033-0.09680.126-0.0014-0.0030.12750.01210.139111.3206158.468296.685
51.19180.33390.41630.6681-0.08571.20730.0676-0.1814-0.13090.1274-0.0316-0.0486-0.0498-0.0128-0.030.1435-0.0049-0.02570.14780.01730.107617.1048160.1133108.4662
62.2662.17670.84692.90631.81291.53430.2389-0.2358-0.87380.2144-0.1276-0.24810.5295-0.04350.00240.26120.0261-0.05420.12220.0590.43116.2783141.0749106.5222
71.8895-0.2392-0.18941.44320.09761.7497-0.20520.4072-0.32020.04470.23220.05410.3139-0.3353-0.02460.2481-0.05210.02280.1432-0.01590.2651.0155142.332197.9441
82.86013.0654-1.36643.1443-1.52240.5258-0.00890.0626-0.55640.4676-0.1736-0.4293-0.1927-0.00040.15650.2681-0.03250.02720.215-0.02350.3482-16.0644138.3684107.238
92.62671.5755-1.97051.6222-0.07074.02630.50940.18130.1021-0.4614-0.0749-0.25950.06720.1346-0.26040.30890.0101-0.01170.25990.06110.2541-26.9859116.2062128.3521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 51 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 77 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 122 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 169 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 185 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 207 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 232 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 233 through 248 )A0

+
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