[English] 日本語
Yorodumi
- PDB-3hj3: Crystal Structure of the ChTS-DHFR F207A Non-Active Site Mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hj3
TitleCrystal Structure of the ChTS-DHFR F207A Non-Active Site Mutant
ComponentsChain A, crystal structure of Dhfr
KeywordsOXIDOREDUCTASE / TS / DHFR / ENZYME / CROSSOVER / NON-ACTIVE SITE
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 / METHOTREXATE / Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / :
Similarity search - Component
Biological speciesCryptosporidium hominis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAnderson, K.S. / Martucci, W.E.
CitationJournal: Medchemcomm / Year: 2013
Title: Exploring novel strategies for AIDS protozoal pathogens: alpha-helix mimetics targeting a key allosteric protein-protein interaction in C. hominis TS-DHFR.
Authors: Martucci, W.E. / Rodriguez, J.M. / Vargo, M.A. / Marr, M. / Hamilton, A.D. / Anderson, K.S.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Jan 15, 2014Group: Database references
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Oct 13, 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 1.7Sep 6, 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: Chain A, crystal structure of Dhfr
B: Chain A, crystal structure of Dhfr
C: Chain A, crystal structure of Dhfr
D: Chain A, crystal structure of Dhfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,90218
Polymers240,7464
Non-polymers7,15614
Water4,810267
1
A: Chain A, crystal structure of Dhfr
B: Chain A, crystal structure of Dhfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,34410
Polymers120,3732
Non-polymers3,9718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16180 Å2
ΔGint-45 kcal/mol
Surface area38640 Å2
MethodPISA
2
C: Chain A, crystal structure of Dhfr
D: Chain A, crystal structure of Dhfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5588
Polymers120,3732
Non-polymers3,1856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14570 Å2
ΔGint-39 kcal/mol
Surface area39480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.860, 121.860, 342.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Chain A, crystal structure of Dhfr


Mass: 60186.426 Da / Num. of mol.: 4 / Mutation: F207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Gene: Chro.40506 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CGA3

-
Non-polymers , 5 types, 281 molecules

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


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


Mass: 477.469 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Chemical
ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.04M ammonium sulfate, 0.12M lithium sulfate, 0.1M Tris, 16% PEG 6000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2008
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 81237 / Num. obs: 77069 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.6 / % possible all: 95

-
Processing

Software
NameClassification
CNSrefinement
AMoREphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZF

1qzf


Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 4070 -random
Rwork0.228 ---
all0.228 77069 --
obs0.228 77069 99.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16526 0 489 267 17282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d2.24
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.384 635 -
Rwork0.319 --
obs-12184 95.5 %

+
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