[English] 日本語
Yorodumi
- PDB-9svn: Structure of dihydrofolate reductase from Burkholderia thailanden... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9svn
TitleStructure of dihydrofolate reductase from Burkholderia thailandensis (I99L variant) complexed with trimethoprim and dihydrofolate
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / thymine synthesis tetrahydrofolate
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / one-carbon metabolic process / tetrahydrofolate biosynthetic process / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-NDP / TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsMechulam, Y. / Schmitt, E. / Lazennec-Schurdevin, C.
Funding support France, 1items
OrganizationGrant numberCountry
Other government2020 65 00 57 France
CitationJournal: Acs Infect Dis. / Year: 2026
Title: Evolutionary Convergence on a Dihydrofolate Reductase Mutation Drives Trimethoprim-Sulfamethoxazole Resistance in Burkholderia thailandensis.
Authors: Guillier, S. / Lazennec-Schurdevin, C. / Mondange, L. / Sarilar, V. / Marchandeau, M. / Lemoigne, C. / Lamer, O. / Lescat, M. / Schmitt, E. / Mechulam, Y. / Garrec, J. / Biot, F.
History
DepositionOct 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,68526
Polymers92,4505
Non-polymers6,23521
Water5,242291
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7185
Polymers18,4901
Non-polymers1,2284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6224
Polymers18,4901
Non-polymers1,1323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9107
Polymers18,4901
Non-polymers1,4206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6224
Polymers18,4901
Non-polymers1,1323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8146
Polymers18,4901
Non-polymers1,3245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.306, 118.306, 146.034
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Space group name HallP32
Components on special symmetry positions
IDModelComponents
11C-206-

SO4

21A-378-

HOH

-
Components

#1: Protein
Dihydrofolate reductase


Mass: 18489.941 Da / Num. of mol.: 5 / Mutation: I99L
Source method: isolated from a genetically manipulated source
Details: GSM sequence added at the N-terminus due to removal of the His-tag by thrombin cleavage.
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: C7S16_1590 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAW9D207, dihydrofolate reductase
#2: Chemical
ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H18N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 8000 0.2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.19→48.68 Å / Num. obs: 59941 / % possible obs: 99.9 % / Redundancy: 21 % / CC1/2: 0.999 / Net I/σ(I): 11.61
Reflection shellResolution: 2.19→2.33 Å / Redundancy: 20.9 % / Num. unique obs: 9590 / CC1/2: 0.419 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→48.68 Å / Cross valid method: FREE R-VALUE / σ(F): 398.51 / Phase error: 25.6024
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 2997 5.02 %
Rwork0.2168 56745 -
obs0.218 59742 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.67 Å2
Refinement stepCycle: LAST / Resolution: 2.19→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6413 0 400 291 7104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716958
X-RAY DIFFRACTIONf_angle_d0.86369485
X-RAY DIFFRACTIONf_chiral_restr0.0481004
X-RAY DIFFRACTIONf_plane_restr0.00551397
X-RAY DIFFRACTIONf_dihedral_angle_d25.1082714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.230.57441520.56072744X-RAY DIFFRACTION91.38
2.23-2.270.46011470.5492758X-RAY DIFFRACTION93.87
2.27-2.320.61430.46022849X-RAY DIFFRACTION95.13
2.32-2.360.471490.40752790X-RAY DIFFRACTION94.93
2.36-2.420.44481430.40352876X-RAY DIFFRACTION95.26
2.42-2.470.35471430.35442808X-RAY DIFFRACTION95.12
2.47-2.530.39371400.32632806X-RAY DIFFRACTION95.25
2.53-2.60.32821580.31632829X-RAY DIFFRACTION94.71
2.6-2.680.34241450.32862X-RAY DIFFRACTION95.18
2.68-2.770.37121390.28172851X-RAY DIFFRACTION95.35
2.77-2.860.2811590.24022806X-RAY DIFFRACTION94.64
2.86-2.980.23611390.23592836X-RAY DIFFRACTION95.33
2.98-3.110.25311470.22762858X-RAY DIFFRACTION95.11
3.11-3.280.22231500.22592823X-RAY DIFFRACTION94.95
3.28-3.480.2581530.21142874X-RAY DIFFRACTION94.91
3.48-3.750.24841360.19612849X-RAY DIFFRACTION95.44
3.75-4.130.20191470.17772838X-RAY DIFFRACTION95.08
4.13-4.730.19371650.1432877X-RAY DIFFRACTION94.58
4.73-5.950.20221630.15732868X-RAY DIFFRACTION94.62
5.95-48.680.1961770.18062945X-RAY DIFFRACTION94.27
Refinement TLS params.Method: refined / Origin x: 37.4084116073 Å / Origin y: 5.27755556881 Å / Origin z: 46.3439708634 Å
111213212223313233
T0.426733652813 Å2-0.00487821614039 Å2-0.00581375908852 Å2-0.410686782735 Å2-0.0163981504523 Å2--0.306951369485 Å2
L0.105461272011 °20.0500621714128 °20.106475225404 °2--0.0315314653722 °20.020221142156 °2--0.0599836896578 °2
S0.0304250387567 Å °0.0158024141399 Å °-0.00674104883333 Å °-0.0113961011481 Å °-0.00982909712879 Å °0.012240797695 Å °0.0267535354477 Å °-0.0222647737094 Å °5.35161485012E-6 Å °
Refinement TLS groupSelection details: 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://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