[English] 日本語
Yorodumi
- PDB-8evn: Sulfatase from Mycobacterium tuberculosis (Rv3406) in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8evn
TitleSulfatase from Mycobacterium tuberculosis (Rv3406) in complex with N-oxalylglycine (NOG)
ComponentsAlpha-ketoglutarate-dependent sulfate ester dioxygenase
KeywordsOXIDOREDUCTASE/INHIBITOR / oxidoreductase-inhibitor complex / sulfatase / 2-oxoglutarate dependent dioxygenase
Function / homology
Function and homology information


alkyl sulfatase / 2-oxoglutarate-dependent dioxygenase activity / response to antibiotic / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Alpha-ketoglutarate-dependent sulfate ester dioxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.644 Å
AuthorsJuan, T.-J. / Leung, I. / Squire, C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Not funded New Zealand
CitationJournal: To Be Published
Title: Sulfatase from Mycobacterium tuberculosis (Rv3406) in complex with inhibitors NOG and FG2216
Authors: Juan, T.-J. / Leung, I. / Squire, C.J.
History
DepositionOct 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
B: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
C: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
D: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,55013
Polymers131,6054
Non-polymers9459
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-74 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.535, 128.336, 138.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Alpha-ketoglutarate-dependent sulfate ester dioxygenase / Type II alkyl sulfatase


Mass: 32901.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3406, MTCY78.22c / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli)
References: UniProt: P9WKZ1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical
ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16% PEG2000, 100 mM Tris, pH 8.5, 2% MPD, 300 mM magnesium nitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.64→47.676 Å / Num. obs: 34771 / % possible obs: 99.2 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 11.9
Reflection shellResolution: 2.64→2.77 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4332 / CC1/2: 0.86 / Rpim(I) all: 0.381 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FFA

4ffa


Resolution: 2.644→47.676 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 48.609 / SU ML: 0.422 / Cross valid method: FREE R-VALUE / ESU R: 0.944 / ESU R Free: 0.381
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 1734 5.006 %random selection
Rwork0.2502 32901 --
all0.253 ---
obs-34635 98.988 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 85.363 Å2
Baniso -1Baniso -2Baniso -3
1-13.329 Å20 Å2-0 Å2
2---6.662 Å20 Å2
3----6.667 Å2
Refinement stepCycle: LAST / Resolution: 2.644→47.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7227 0 52 13 7292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166589
X-RAY DIFFRACTIONr_angle_refined_deg0.6411.63310161
X-RAY DIFFRACTIONr_angle_other_deg0.2411.55115230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4155931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2211066
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.598101073
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.45410346
X-RAY DIFFRACTIONr_chiral_restr0.0290.21148
X-RAY DIFFRACTIONr_chiral_restr_other0.0210.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021529
X-RAY DIFFRACTIONr_nbd_refined0.1720.21377
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.26604
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23555
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2162
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0840.23
X-RAY DIFFRACTIONr_nbd_other0.0920.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.21
X-RAY DIFFRACTIONr_mcbond_it0.7015.5243761
X-RAY DIFFRACTIONr_mcbond_other0.75.5233760
X-RAY DIFFRACTIONr_mcangle_it1.2128.2824679
X-RAY DIFFRACTIONr_mcangle_other1.2128.2824680
X-RAY DIFFRACTIONr_scbond_it1.2195.6243702
X-RAY DIFFRACTIONr_scbond_other1.2175.6243702
X-RAY DIFFRACTIONr_scangle_it1.1878.3895482
X-RAY DIFFRACTIONr_scangle_other1.1878.395483
X-RAY DIFFRACTIONr_lrange_it2.57865.6847913
X-RAY DIFFRACTIONr_lrange_other2.57865.697914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.644-2.7130.52970.47320870.47525220.5810.71286.59790.471
2.713-2.7870.431310.41923500.4224810.7820.7421000.41
2.787-2.8670.431090.38923140.3924230.7680.7851000.372
2.867-2.9550.4251190.36922150.37123340.840.8171000.349
2.955-3.0520.3461310.34221420.34222730.8650.861000.314
3.052-3.1590.311140.29720900.29822040.9010.9131000.269
3.159-3.2770.3221130.27320410.27621540.9370.941000.248
3.277-3.410.3111050.24219170.24620220.9220.9591000.221
3.41-3.5610.282970.24518770.24619740.9490.9621000.223
3.561-3.7340.275820.22918070.23118900.9480.96699.94710.211
3.734-3.9350.23850.21417080.21517930.9670.9721000.194
3.935-4.1720.21720.19416500.19417220.9730.9771000.177
4.172-4.4570.23830.19515300.19716130.9670.9771000.186
4.457-4.8110.223680.1914400.19215080.9620.9771000.186
4.811-5.2650.284950.21812990.22213940.9560.9691000.213
5.265-5.8770.36660.26112210.26612870.9420.9561000.251
5.877-6.7690.38650.28510660.2911310.930.9511000.279
6.769-8.2490.358260.2459560.2489820.9060.9611000.253
8.249-11.4950.224450.1987320.1997770.9690.9761000.221
11.495-47.6760.347310.2844590.2884910.9260.93599.79630.298
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)
11.1301-0.68460.5344.3565-0.53391.69420.2101-0.0705-0.0750.02090.003-0.23670.47050.2208-0.2130.28390.0787-0.1960.3821-0.04190.155713.1773-9.771-11.6797
21.8651-0.88840.19243.373-0.00762.5837-0.1447-0.3943-0.12130.90910.28850.33110.0774-0.2859-0.14390.28970.06760.0520.4688-0.04620.08660.513.82865.525
31.1943-0.25670.94784.1857-1.35934.2457-0.0146-0.0787-0.2466-0.67440.34160.90520.3184-0.3486-0.3270.2011-0.1042-0.20520.38240.07510.2989-11.736617.5224-41.5417
41.0695-0.02180.65153.57090.11725.2348-0.21180.3720.1348-0.51340.1867-0.5843-0.31851.01480.02510.1272-0.16830.05870.6548-0.03330.147314.40632.3446-35.4628
Refinement TLS groupSelection: ALL

+
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://pdbjlvh1.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