[English] 日本語
Yorodumi
- PDB-3v3n: Crystal structure of TetX2 T280A: an adaptive mutant in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v3n
TitleCrystal structure of TetX2 T280A: an adaptive mutant in complex with minocycline
ComponentsTetX2 protein
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / Rossmann Fold / tetracycline degrading monooxygenase / OXIDOREDUCTASE-ANTIBIOTIC complex
Function / homology
Function and homology information


tetracycline 11a-monooxygenase / FAD binding / monooxygenase activity / response to antibiotic / cytoplasm
Similarity search - Function
Flavin-dependent monooxygenase TetX / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-MIY / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.703 Å
AuthorsWalkiewicz, K. / Shamoo, Y.
CitationJournal: To be Published
Title: Crystal structure of TetX2 T280A: an adaptive mutant in complex with minocycline
Authors: Walkiewicz, K. / Shamoo, Y.
History
DepositionDec 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: TetX2 protein
B: TetX2 protein
C: TetX2 protein
D: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,74920
Polymers170,0094
Non-polymers5,74116
Water2,702150
1
A: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.426, 80.102, 87.362
Angle α, β, γ (deg.)111.11, 90.10, 93.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 14:246 or resseq 250:382 )
21chain B and (resseq 14:246 or resseq 250:382 )
31chain C and (resseq 14:246 or resseq 250:382 )
41chain D and (resseq 14:246 or resseq 250:382 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYSchain 'A' and (resseq 14:246 or resseq 250:382 )AA14 - 2464 - 236
12GLNGLNPHEPHEchain 'A' and (resseq 14:246 or resseq 250:382 )AA250 - 382240 - 372
21LEULEULYSLYSchain 'B' and (resseq 14:246 or resseq 250:382 )BB14 - 2464 - 236
22GLNGLNPHEPHEchain 'B' and (resseq 14:246 or resseq 250:382 )BB250 - 382240 - 372
31LEULEULYSLYSchain 'C' and (resseq 14:246 or resseq 250:382 )CC14 - 2464 - 236
32GLNGLNPHEPHEchain 'C' and (resseq 14:246 or resseq 250:382 )CC250 - 382240 - 372
41LEULEULYSLYSchain 'D' and (resseq 14:246 or resseq 250:382 )DD14 - 2464 - 236
42GLNGLNPHEPHEchain 'D' and (resseq 14:246 or resseq 250:382 )DD250 - 382240 - 372

NCS oper:
IDCodeMatrixVector
1given(-0.999155, 0.013139, -0.038949), (0.0001, -0.946756, -0.321951), (-0.041105, -0.321683, 0.945955)-38.838001, -18.172701, -3.82157
2given(-0.999446, -0.004031, 0.033027), (0.006816, 0.946773, 0.321829), (-0.032567, 0.321876, -0.946222)-8.49614, -58.584, -23.679399
3given(0.999993, -0.00194, -0.003083), (-0.00194, -0.999998, 0.00017), (-0.003083, -0.000164, -0.999995)34.214802, -35.099201, -7.09053

-
Components

#1: Protein
TetX2 protein


Mass: 42502.141 Da / Num. of mol.: 4 / Fragment: TetX2 protein / Mutation: T280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: Bacteroides thetaiotaomicron / Gene: tetX2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q93L51
#2: Chemical
ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE


Mass: 457.476 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H27N3O7 / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: Ammonium Sulafate, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00004 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 13, 2011
Details: Rosenbaum-Rock Si (111) sagitally focused monochromator
RadiationMonochromator: Rosenbaum-Rock Si (111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.703→50 Å / Num. obs: 43415 / % possible obs: 93 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.703-2.771.50.317184.7
2.77-2.821.60.302189.7
2.82-2.871.60.284192.2
2.87-2.931.60.233194.1
2.93-2.991.60.205192.6
2.99-3.061.60.175194.6
3.06-3.141.60.164192.4
3.14-3.221.60.137192.7
3.22-3.321.70.118192.5
3.32-3.431.70.113190.6
3.43-3.551.70.096192.5
3.55-3.691.70.092191.5
3.69-3.861.80.088193.3
3.86-4.061.80.083192.8
4.06-4.321.90.077192.7
4.32-4.651.90.066192.5
4.65-5.121.90.061195.5
5.12-5.861.90.061197
5.86-7.381.90.055198.2
7.38-501.90.048197.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å49.3 Å
Translation2.7 Å49.3 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P9U

3p9u


Resolution: 2.703→49.297 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.87 / σ(F): 0.06 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1896 4.61 %RANDOM
Rwork0.2208 ---
obs0.2233 41120 87.01 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.317 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5001 Å2-1.5437 Å2-0.0816 Å2
2--8.6507 Å29.3194 Å2
3----10.1508 Å2
Refinement stepCycle: LAST / Resolution: 2.703→49.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11559 0 384 150 12093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912199
X-RAY DIFFRACTIONf_angle_d1.23516573
X-RAY DIFFRACTIONf_dihedral_angle_d18.4184541
X-RAY DIFFRACTIONf_chiral_restr0.0791797
X-RAY DIFFRACTIONf_plane_restr0.0042145
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2874X-RAY DIFFRACTIONPOSITIONAL0.044
12B2874X-RAY DIFFRACTIONPOSITIONAL0.044
13C2874X-RAY DIFFRACTIONPOSITIONAL0.048
14D2874X-RAY DIFFRACTIONPOSITIONAL0.028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.703-2.77060.4473950.33491844X-RAY DIFFRACTION58
2.7706-2.84550.39051080.30682552X-RAY DIFFRACTION78
2.8455-2.92920.35281370.28952594X-RAY DIFFRACTION82
2.9292-3.02370.38111330.27022710X-RAY DIFFRACTION85
3.0237-3.13180.28341350.25752870X-RAY DIFFRACTION88
3.1318-3.25720.32491340.23232877X-RAY DIFFRACTION89
3.2572-3.40540.27431450.22082869X-RAY DIFFRACTION90
3.4054-3.58490.28041430.21062873X-RAY DIFFRACTION90
3.5849-3.80940.25791490.20412946X-RAY DIFFRACTION90
3.8094-4.10340.2341370.19422903X-RAY DIFFRACTION91
4.1034-4.51610.22081390.17642930X-RAY DIFFRACTION91
4.5161-5.16890.21551390.1853011X-RAY DIFFRACTION94
5.1689-6.50990.28471510.21633114X-RAY DIFFRACTION97
6.5099-49.30510.27951510.23813131X-RAY DIFFRACTION97

+
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