[English] 日本語
Yorodumi
- PDB-4glt: Crystal structure of glutathione s-transferase MFLA_2116 (target ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4glt
TitleCrystal structure of glutathione s-transferase MFLA_2116 (target EFI-507160) from methylobacillus flagellatus kt with gsh bound
ComponentsGlutathione S-transferase-like protein
KeywordsTRANSFERASE / TRANSFERASE-LIKE PROTEIN / STRUCTURAL GENOMICS / ENZYME FUNCTION INITIATIVE / EFI
Function / homology
Function and homology information


transferase activity / cytoplasm
Similarity search - Function
: / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...: / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase-like protein
Similarity search - Component
Biological speciesMethylobacillus flagellatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of glutathione s-transferase MFLA_2116 (target EFI-507160) from methylobacillus flagellatus kt with gsh bound
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-transferase-like protein
B: Glutathione S-transferase-like protein
C: Glutathione S-transferase-like protein
D: Glutathione S-transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4598
Polymers102,2304
Non-polymers1,2294
Water1,26170
1
A: Glutathione S-transferase-like protein
B: Glutathione S-transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7294
Polymers51,1152
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-24 kcal/mol
Surface area18830 Å2
MethodPISA
2
C: Glutathione S-transferase-like protein
D: Glutathione S-transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7294
Polymers51,1152
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-24 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.815, 97.024, 81.868
Angle α, β, γ (deg.)90.00, 105.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVALAA0 - 20122 - 223
21SERSERVALVALBB0 - 20122 - 223
12SERSERPROPROAA0 - 20022 - 222
22SERSERPROPROCC0 - 20022 - 222
13ASNASNILEILEAA-5 - 20217 - 224
23ASNASNILEILEDD-5 - 20217 - 224
14SERSERPROPROBB0 - 20022 - 222
24SERSERPROPROCC0 - 20022 - 222
15SERSERVALVALBB0 - 20122 - 223
25SERSERVALVALDD0 - 20122 - 223
16SERSERPROPROCC0 - 20022 - 222
26SERSERPROPRODD0 - 20022 - 222

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Glutathione S-transferase-like protein


Mass: 25557.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus (bacteria) / Strain: KT / Gene: Mfla_2116 / References: UniProt: Q1GZF4
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growpH: 7.5
Details: 0.2M POTASSIUM ACETATE, PH 7.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2012 / Details: MIRRORS
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.2→70 Å / Num. obs: 42092 / % possible obs: 99.3 % / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.067 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.2 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0025refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TOU

3tou


Resolution: 2.2→46.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.996 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28251 1313 3.2 %RANDOM
Rwork0.20897 ---
obs0.21139 40311 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å25.1 Å2
2---2.36 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 80 70 6659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196744
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.061.989137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2355819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22923.182308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.689151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6411565
X-RAY DIFFRACTIONr_chiral_restr0.0670.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215107
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2280.32
12B2280.32
21A2320.29
22C2320.29
31A2360.28
32D2360.28
41B2330.32
42C2330.32
51B2310.31
52D2310.31
61C2300.28
62D2300.28
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 92 -
Rwork0.33 2810 -
obs--94.07 %
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)
12.84020.277-0.57093.3151-0.26832.4005-0.025-0.13840.140.26680.10160.2654-0.0766-0.2419-0.07650.1829-0.031-0.06670.31110.00860.124-34.412-12.18785.6689
22.9987-0.1005-0.70073.9609-0.29633.8857-0.0346-0.04440.0735-0.22690.0495-0.4310.13340.2478-0.01490.1392-0.0493-0.0720.2459-0.01560.1337-16.0112-15.5605-6.8188
33.5581-0.476-0.51292.7691-0.06084.32220.01370.0204-0.3324-0.2004-0.2949-0.49430.30720.46920.28120.18110.1016-0.06030.31670.07830.2428-17.1138-3.206241.3648
43.139-0.7605-0.76782.1960.16214.58680.15320.24710.2153-0.0032-0.15560.245-0.3365-0.03340.00240.14860.0457-0.0940.21760.00750.1594-35.85629.104139.9208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 202
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 417
4X-RAY DIFFRACTION2B0 - 202
5X-RAY DIFFRACTION2B301
6X-RAY DIFFRACTION2B401 - 418
7X-RAY DIFFRACTION3C0 - 201
8X-RAY DIFFRACTION3C301
9X-RAY DIFFRACTION3C401 - 417
10X-RAY DIFFRACTION4D-5 - 202
11X-RAY DIFFRACTION4D301
12X-RAY DIFFRACTION4D401 - 418

+
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