[English] 日本語
Yorodumi
- PDB-3sa2: Bacuills anthracis Dihydrofolate Reductase bound propargyl-linked... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sa2
TitleBacuills anthracis Dihydrofolate Reductase bound propargyl-linked TMP analog, UCP1014
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7DR / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAnderson, A.C. / Beierlein, J.M.
CitationJournal: to be published
Title: SAR studies of heterocyclic propargyl-linked TMP analogs to Bacillus dihydrofolate reductase
Authors: Anderson, A.C. / Beierlein, J.M. / Viswanathan, K. / Wright, D.L.
History
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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 / 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: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4186
Polymers39,2152
Non-polymers2,2044
Water2,108117
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7093
Polymers19,6071
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7093
Polymers19,6071
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.265, 78.265, 66.997
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASPASPBB1 - 104 - 13
21METMETASPASPAA1 - 104 - 13
12ASPASPLEULEUBB18 - 2921 - 32
22ASPASPLEULEUAA18 - 2921 - 32
13TYRTYRVALVALBB31 - 3234 - 35
23TYRTYRVALVALAA31 - 3234 - 35
14THRTHRTHRTHRBB35 - 3638 - 39
24THRTHRTHRTHRAA35 - 3638 - 39
15GLYGLYGLUGLUBB38 - 9041 - 93
25GLYGLYGLUGLUAA38 - 9041 - 93
16GLUGLUPROPROBB92 - 12895 - 131
26GLUGLUPROPROAA92 - 12895 - 131
17GLUGLUGLNGLNBB137 - 161140 - 164
27GLUGLUGLNGLNAA137 - 161140 - 164
18ASNASNGLYGLYBB12 - 1615 - 19
28ASNASNGLYGLYAA12 - 1615 - 19

-
Components

#1: Protein Dihydrofolate reductase


Mass: 19607.330 Da / Num. of mol.: 2 / Mutation: I2R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS2083, BA_2237, dfrA, GBAA2237, GBAA_2237 / Plasmid: PQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q81R22, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-7DR / 6-ethyl-5-[3-(5-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-2,4-diamine


Mass: 358.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 52.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: initial crystal hits were grown in 27.5% (w/v) PEG 10,000, 0.1 M MES, pH 6.50, at an equal ratio of protein to crystallization solution. Microseeding was used to obtain isolated crystals in ...Details: initial crystal hits were grown in 27.5% (w/v) PEG 10,000, 0.1 M MES, pH 6.50, at an equal ratio of protein to crystallization solution. Microseeding was used to obtain isolated crystals in 10% (w/v) PEG 10,000 and 0.1 MES, pH 6.50 at a protein concentration of 5 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→42.67 Å / Num. obs: 19128 / % possible obs: 98.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 2.9 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 12.6
Reflection shellResolution: 2.25→2.308 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3 / Num. unique all: 1330 / Rsym value: 0.353 / % possible all: 99.01

-
Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.8Ldata scaling
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→42.67 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 6.637 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 978 5.1 %RANDOM
Rwork0.2336 ---
all0.2347 ---
obs0.2347 18150 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.37 Å2 / Biso mean: 26.0644 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 150 117 3027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223023
X-RAY DIFFRACTIONr_angle_refined_deg1.24424109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02623.806155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34715499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0091517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212327
X-RAY DIFFRACTIONr_mcbond_it0.5271.51651
X-RAY DIFFRACTIONr_mcangle_it0.99822687
X-RAY DIFFRACTIONr_scbond_it1.21331372
X-RAY DIFFRACTIONr_scangle_it2.0384.51419
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
581TIGHT POSITIONAL0.030.05
609LOOSE POSITIONAL0.035
581TIGHT THERMAL0.060.5
609LOOSE THERMAL0.0810
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 77 -
Rwork0.307 1330 -
all-1407 -
obs--99.01 %

+
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