[English] 日本語
Yorodumi
- PDB-2on7: Structure of NaGST-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2on7
TitleStructure of NaGST-1
ComponentsNa Glutathione S-transferase 1
KeywordsTRANSFERASE / GST / hookworm / Necator
Function / homologyGlutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Function and homology information
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAsojo, O.A. / Ngamelue, M. / Homma, H. / Goud, G. / Zhan, B. / Hotez, P.J.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: X-ray structures of Na-GST-1 and Na-GST-2 two glutathione s-transferase from the human hookworm Necator americanus
Authors: Asojo, O.A. / Homma, K. / Sedlacek, M. / Ngamelue, M. / Goud, G.N. / Zhan, B. / Deumic, V. / Asojo, O. / Hotez, P.J.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / 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.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Na Glutathione S-transferase 1
B: Na Glutathione S-transferase 1
C: Na Glutathione S-transferase 1
D: Na Glutathione S-transferase 1


Theoretical massNumber of molelcules
Total (without water)94,8414
Polymers94,8414
Non-polymers00
Water4,216234
1
A: Na Glutathione S-transferase 1
D: Na Glutathione S-transferase 1


Theoretical massNumber of molelcules
Total (without water)47,4212
Polymers47,4212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na Glutathione S-transferase 1
C: Na Glutathione S-transferase 1


Theoretical massNumber of molelcules
Total (without water)47,4212
Polymers47,4212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.975, 80.683, 200.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 1 - 206 / Label seq-ID: 1 - 206

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Na Glutathione S-transferase 1 / NaGST-1


Mass: 23710.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Necator americanus (New World hookworm)
Plasmid: pPICZaA / Production host: Pichia pastoris (fungus)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG, acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 47226 / Num. obs: 47226 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 31.81 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.067 / Net I/σ(I): 19.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3106 / Rsym value: 0.256 / % possible all: 66.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1TW9

1tw9


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.886 / SU B: 10.997 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.752 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28353 1611 5 %RANDOM
Rwork0.18951 ---
all0.19418 ---
obs0.19418 30348 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.589 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 0 234 6930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9719252
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91823.827324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.593151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8191540
X-RAY DIFFRACTIONr_chiral_restr0.1280.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.23277
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24673
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.2192
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.277
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6831.54223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09326632
X-RAY DIFFRACTIONr_scbond_it2.03632988
X-RAY DIFFRACTIONr_scangle_it2.8564.52620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A824medium positional0.320.5
2B824medium positional0.360.5
3C824medium positional0.450.5
4D824medium positional0.350.5
1A850loose positional0.825
2B850loose positional0.855
3C850loose positional1.135
4D850loose positional0.985
1A824medium thermal0.892
2B824medium thermal0.82
3C824medium thermal0.862
4D824medium thermal0.752
1A850loose thermal2.1610
2B850loose thermal2.0510
3C850loose thermal2.2710
4D850loose thermal2.2310
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 109 -
Rwork0.174 2181 -
obs--98.96 %
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)
12.6606-0.723-0.59031.59390.14654.257-0.10090.2459-0.186-0.0958-0.10640.17180.1176-0.37110.2073-0.17670.05360.0163-0.13170.0189-0.1296-1.396855.056263.2763
23.1824-0.8993-1.44851.9737-0.4096.1468-0.07340.3833-0.1599-0.0173-0.04190.1974-0.1079-0.68330.1153-0.19480.07450.0193-0.0547-0.0008-0.1602-25.989315.51763.0114
32.0302-0.6942-0.33153.2067-1.07943.9125-0.0982-0.0262-0.17730.1671-0.125-0.00040.1471-0.14550.2232-0.12710.05940.0074-0.19560.035-0.1667-21.2416.709986.6693
41.8265-0.7953-0.23113.2795-0.92913.7778-0.0982-0.104-0.21050.0848-0.16940.05340.23380.05940.2676-0.10870.08520.0287-0.17090.0568-0.13713.675847.494487.0586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2061 - 206
2X-RAY DIFFRACTION2BB1 - 2061 - 206
3X-RAY DIFFRACTION3CC1 - 2061 - 206
4X-RAY DIFFRACTION4DD1 - 2061 - 206

+
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