[English] 日本語
Yorodumi
- PDB-3eem: Candida glabrata Dihydrofolate Reductase complexed with 2,4-diami... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eem
TitleCandida glabrata Dihydrofolate Reductase complexed with 2,4-diamino-5-[3-methyl-3-(3-methoxy-5-(2,6-dimethylphenyl)phenyl)prop-1-ynyl]-6-methylpyrimidine(UCP111D26M) and NADPH
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / enzyme
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 / mitochondrion
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-53V / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 Å
AuthorsLiu, J. / Anderson, A.
CitationJournal: Chem.Biol.Drug Des. / Year: 2009
Title: Probing the active site of Candida glabrata dihydrofolate reductase with high resolution crystal structures and the synthesis of new inhibitors
Authors: Liu, J. / Bolstad, D.B. / Smith, A.E. / Priestley, N.D. / Wright, D.L. / Anderson, A.C.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 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_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_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)55,1186
Polymers52,8552
Non-polymers2,2644
Water3,693205
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5593
Polymers26,4271
Non-polymers1,1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5593
Polymers26,4271
Non-polymers1,1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.822, 42.822, 231.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13B
23A
14B
24A
15B
25A
16B
26A

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASPASPAA153 - 154153 - 154
21METMETASPASPBB153 - 154153 - 154
12GLUGLUGLNGLNAA161 - 164161 - 164
22GLUGLUGLNGLNBB161 - 164161 - 164
13LEULEUGLNGLNBB105 - 106105 - 106
23LEULEUGLNGLNAA105 - 106105 - 106
14ASNASNGLUGLUBB111 - 112111 - 112
24ASNASNGLUGLUAA111 - 112111 - 112
15THRTHRTHRTHRBB148 - 149148 - 149
25THRTHRTHRTHRAA148 - 149148 - 149
16ASNASNSERSERBB46 - 4746 - 47
26ASNASNSERSERAA46 - 4746 - 47

NCS ensembles :
ID
1
2
3
4
5
6
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Dihydrofolate reductase


Mass: 26427.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0J03894g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FPH0
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-53V / 5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine


Mass: 386.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H26N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorDetector: CCD / Date: Feb 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 22825 / % possible obs: 95.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.075 / Χ2: 1.999 / Net I/σ(I): 25.726
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.11-2.194.10.21822830.711195.7
2.19-2.274.30.19423290.957196.5
2.27-2.384.30.15823410.951197.5
2.38-2.54.40.14422941.299197
2.5-2.664.30.12523521.578196.6
2.66-2.864.40.1122631.861195.8
2.86-3.154.40.09322582.538194.6
3.15-3.614.50.07622353.286193.5
3.61-4.544.60.06421824.125190.6
4.54-504.80.04122882.415193.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.11→42.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 5.305 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1159 5.1 %RANDOM
Rwork0.169 ---
obs0.172 22747 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.93 Å2 / Biso mean: 25.549 Å2 / Biso min: 8.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.11→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 154 205 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223948
X-RAY DIFFRACTIONr_angle_refined_deg2.39225360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg31.2565448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65624.086186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01915694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.651524
X-RAY DIFFRACTIONr_chiral_restr0.1970.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022958
X-RAY DIFFRACTIONr_nbd_refined0.2320.21684
X-RAY DIFFRACTIONr_nbtor_refined0.310.22538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.216
X-RAY DIFFRACTIONr_mcbond_it1.621.52365
X-RAY DIFFRACTIONr_mcangle_it1.86623646
X-RAY DIFFRACTIONr_scbond_it3.39331938
X-RAY DIFFRACTIONr_scangle_it4.6724.51714
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A8TIGHT POSITIONAL0.070.05
1A8LOOSE POSITIONAL0.115
1A8TIGHT THERMAL0.180.5
1A8LOOSE THERMAL1.1910
2A16TIGHT POSITIONAL0.070.05
2A19LOOSE POSITIONAL0.415
2A16TIGHT THERMAL0.160.5
2A19LOOSE THERMAL1.4610
3B8TIGHT POSITIONAL0.080.05
3B9LOOSE POSITIONAL0.115
3B8TIGHT THERMAL0.190.5
3B9LOOSE THERMAL0.8710
4B8TIGHT POSITIONAL0.080.05
4B9LOOSE POSITIONAL0.565
4B8TIGHT THERMAL0.10.5
4B9LOOSE THERMAL0.7710
5B8TIGHT POSITIONAL0.090.05
5B6LOOSE POSITIONAL0.175
5B8TIGHT THERMAL0.190.5
5B6LOOSE THERMAL0.9510
6B8TIGHT POSITIONAL0.110.05
6B6LOOSE POSITIONAL0.335
6B8TIGHT THERMAL0.150.5
6B6LOOSE THERMAL0.3710
LS refinement shellResolution: 2.107→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 76 -
Rwork0.181 1590 -
all-1666 -
obs--92.92 %

+
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