[English] 日本語
Yorodumi
- PDB-3dl6: Crystal Structure of the A287F/S290G Active Site Mutant of TS-DHF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dl6
TitleCrystal Structure of the A287F/S290G Active Site Mutant of TS-DHFR from Cryptosporidium hominis
ComponentsDihydrofolate reductase, DHFR
KeywordsOXIDOREDUCTASE / Enzyme active site mutant / Enzyme-ligand complex
Function / homology
Function and homology information


Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / DIHYDROFOLIC ACID / Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / :
Similarity search - Component
Biological speciesCryptosporidium hominis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsMartucci, W.E. / Vargo, M.A. / Anderson, K.S.
CitationJournal: Biochemistry / Year: 2008
Title: Explaining an unusually fast parasitic enzyme: folate tail-binding residues dictate substrate positioning and catalysis in Cryptosporidium hominis thymidylate synthase.
Authors: Martucci, W.E. / Vargo, M.A. / Anderson, K.S.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)311,41525
Polymers301,5435
Non-polymers9,87220
Water2,576143
1
C: Dihydrofolate reductase, DHFR
D: Dihydrofolate reductase, DHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,56610
Polymers120,6172
Non-polymers3,9498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15850 Å2
ΔGint-51 kcal/mol
Surface area39100 Å2
MethodPISA
2
A: Dihydrofolate reductase, DHFR
B: Dihydrofolate reductase, DHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,56610
Polymers120,6172
Non-polymers3,9498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15700 Å2
ΔGint-48 kcal/mol
Surface area38770 Å2
MethodPISA
3
E: Dihydrofolate reductase, DHFR
hetero molecules

E: Dihydrofolate reductase, DHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,56610
Polymers120,6172
Non-polymers3,9498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_457-x-1,y,-z+21
Buried area15780 Å2
ΔGint-45 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.906, 116.921, 220.948
Angle α, β, γ (deg.)90.00, 95.94, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Dihydrofolate reductase, DHFR


Mass: 60308.590 Da / Num. of mol.: 5 / Mutation: A287F,S290G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Gene: Chro.40506 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: Q5CGA3, dihydrofolate reductase

-
Non-polymers , 5 types, 163 molecules

#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Chemical
ChemComp-DHF / DIHYDROFOLIC ACID


Mass: 443.413 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H21N7O6
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 4.58 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1mM ammonium sulfate, 0.2mM, lithium sulfate, 0.1mM Tris, 12% PEG-6000, flash frozen in 25% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.25→46.2 Å / Num. obs: 83352 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.8
Reflection shellResolution: 3.25→3.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.9 / Num. unique all: 11488 / % possible all: 84.8

-
Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZF

1qzf


Resolution: 3.25→3.45 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4159 -random
Rwork0.225 ---
all0.225 83352 --
obs0.225 83352 98.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.25→3.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20628 0 675 143 21446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d2.75
LS refinement shellResolution: 3.25→3.45 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.36 577 -
Rwork0.294 --
obs-11488 84.8 %

+
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