[English] 日本語
Yorodumi
- PDB-3ia4: Moritella profunda dihydrofolate reductase (DHFR) in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ia4
TitleMoritella profunda dihydrofolate reductase (DHFR) in complex with NADPH and methotrexate (MTX)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR dihydrofolate reductase / NADPH / methotrexate
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 / 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
METHOTREXATE / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMoritella profunda (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLevy, C.
CitationJournal: Chembiochem / Year: 2009
Title: Are the Catalytic Properties of Enzymes from Piezophilic Organisms Pressure Adapted?
Authors: Hay, S. / Evans, R.M. / Levy, C. / Loveridge, E.J. / Wang, X. / Leys, D. / Allemann, R.K. / Scrutton, N.S.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Dihydrofolate reductase
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,03512
Polymers73,2354
Non-polymers4,7998
Water17,348963
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5093
Polymers18,3091
Non-polymers1,2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5093
Polymers18,3091
Non-polymers1,2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5093
Polymers18,3091
Non-polymers1,2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5093
Polymers18,3091
Non-polymers1,2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.870, 44.990, 97.370
Angle α, β, γ (deg.)90.00, 114.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Dihydrofolate reductase


Mass: 18308.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moritella profunda (bacteria) / Gene: dyrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70YQ6, dihydrofolate reductase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22N8O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M sodium citrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9696 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 13, 2008
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9696 Å / Relative weight: 1
ReflectionResolution: 1.6→48.3 Å / Num. all: 231614 / Num. obs: 79111 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.77 / Num. unique all: 12422 / % possible all: 94

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.187 Å / SU ML: 0.18 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 3920 5.03 %Random
Rwork0.1543 ---
obs0.1566 77880 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.77 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→44.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5051 0 324 963 6338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195513
X-RAY DIFFRACTIONf_angle_d1.9937562
X-RAY DIFFRACTIONf_dihedral_angle_d22.6341985
X-RAY DIFFRACTIONf_chiral_restr0.148834
X-RAY DIFFRACTIONf_plane_restr0.011944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72070.20881360.17262693X-RAY DIFFRACTION99
1.7207-1.74250.22441460.16752655X-RAY DIFFRACTION100
1.7425-1.76550.22481410.16672687X-RAY DIFFRACTION99
1.7655-1.78960.22331260.1682716X-RAY DIFFRACTION99
1.7896-1.81520.21691610.17342637X-RAY DIFFRACTION100
1.8152-1.84230.22831380.16622684X-RAY DIFFRACTION99
1.8423-1.87110.22691350.16242725X-RAY DIFFRACTION99
1.8711-1.90180.21131490.15722604X-RAY DIFFRACTION99
1.9018-1.93460.2311270.15272711X-RAY DIFFRACTION99
1.9346-1.96970.21741270.1562686X-RAY DIFFRACTION99
1.9697-2.00760.19741340.1472655X-RAY DIFFRACTION99
2.0076-2.04860.2061580.14962666X-RAY DIFFRACTION98
2.0486-2.09310.20021390.15552614X-RAY DIFFRACTION98
2.0931-2.14180.22851550.15672675X-RAY DIFFRACTION98
2.1418-2.19540.19571370.15362603X-RAY DIFFRACTION98
2.1954-2.25480.22221320.14972650X-RAY DIFFRACTION97
2.2548-2.32110.17831570.14862621X-RAY DIFFRACTION97
2.3211-2.3960.19691490.15162597X-RAY DIFFRACTION97
2.396-2.48160.19541360.15882672X-RAY DIFFRACTION97
2.4816-2.5810.21821350.16282590X-RAY DIFFRACTION96
2.581-2.69840.22391310.16822646X-RAY DIFFRACTION96
2.6984-2.84070.22521310.17472636X-RAY DIFFRACTION96
2.8407-3.01860.21031300.16482589X-RAY DIFFRACTION95
3.0186-3.25160.19611450.15052584X-RAY DIFFRACTION94
3.2516-3.57870.17031330.13682587X-RAY DIFFRACTION94
3.5787-4.09630.15941540.12882571X-RAY DIFFRACTION94
4.0963-5.15960.1641370.12452616X-RAY DIFFRACTION94
5.1596-44.20150.1981410.17392590X-RAY DIFFRACTION90

+
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