[English] 日本語
Yorodumi
- PDB-1xcc: 1-Cys peroxidoxin from Plasmodium Yoelli -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1xcc
Title1-Cys peroxidoxin from Plasmodium Yoelli
Components1-Cys peroxiredoxin
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peroxiredoxin activity / cell redox homeostasis / cell
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / Thioredoxin domain / Peroxiredoxin, C-terminal / Peroxiredoxin, AhpC-type / Thioredoxin-like superfamily / AhpC/TSA family / C-terminal domain of 1-Cys peroxiredoxin / Thioredoxin domain profile.
1-Cys peroxiredoxin
Biological speciesPlasmodium yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsVedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Wasney, G. / Amani, M. / Xu, X. / Bray, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Hui, R. / Bochkarev, A. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 2004 / Release: Nov 9, 2004
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 9, 2004Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Feb 14, 2018Structure modelExperimental preparationexptl_crystal_grow_exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1-Cys peroxiredoxin
B: 1-Cys peroxiredoxin
C: 1-Cys peroxiredoxin
D: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)101,3134
Polymers101,3134
Non-polymers00
Water5,765320
1
A: 1-Cys peroxiredoxin
C: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)50,6572
Polymers50,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-32 kcal/mol
Surface area19290 Å2
MethodPISA
2
B: 1-Cys peroxiredoxin
D: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)50,6572
Polymers50,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-29 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)90.390, 156.842, 178.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein/peptide
1-Cys peroxiredoxin


Mass: 25328.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii (eukaryote)
Description: pET15-TEV is a modification of pET15B (Novagen) with thrombin site replaced with TEV site.
Gene: PY04285 / Plasmid: pET15-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q86SB3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 22% Peg 3350, 0.1M Bis-Tris pH 5.5, 0.2M Lithium Sulfate, 5% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97939, 0.97952, 0.96415
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: APS 17ID / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.979521
30.964151
ReflectionResolution: 2.3→20 Å / Num. obs: 53397 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.059 / Net I/σ(I): 24
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.038 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2858 5.1 %RANDOM
Rwork0.183 ---
Obs0.185 53397 99.7 %-
All-53397 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--1.44 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7042 0 0 320 7362
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0220.0227212
r_bond_other_d
r_angle_refined_deg1.8321.9679756
r_angle_other_deg
r_dihedral_angle_1_deg6.9815867
r_dihedral_angle_2_deg39.4225.096314
r_dihedral_angle_3_deg17.601151338
r_dihedral_angle_4_deg15.3331520
r_chiral_restr0.1240.21086
r_gen_planes_refined0.0080.025318
r_gen_planes_other
r_nbd_refined0.2140.23134
r_nbd_other
r_nbtor_refined0.3080.24874
r_nbtor_other
r_xyhbond_nbd_refined0.1610.2399
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.1960.224
r_symmetry_vdw_other
r_symmetry_hbond_refined0.1930.28
r_symmetry_hbond_other
r_mcbond_it1.2061.54506
r_mcbond_other
r_mcangle_it1.96127101
r_scbond_it3.11433149
r_scangle_it4.5794.52655
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 205 -
Rwork0.202 3852 -
Obs--100 %

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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