[English] 日本語
Yorodumi
- PDB-3nrr: Co-crystal structure of dihydrofolate reductase-thymidylate synth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nrr
TitleCo-crystal structure of dihydrofolate reductase-thymidylate synthase from Babesia bovis with dUMP, Raltitrexed and NADP
ComponentsDihydrofolate reductase-thymidylate synthase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / NIAID / dihydrofolate reductase / thymidylate synthase / DHFR / TS / ThyA / oxidoreductase / methyltransferase / Babesiosis / dUMP / NADP / Raltitrexed / Tomudex
Function / homology
Function and homology information


thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase ...Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TOMUDEX / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesBabesia bovis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis.
Authors: Begley, D.W. / Edwards, T.E. / Raymond, A.C. / Smith, E.R. / Hartley, R.C. / Abendroth, J. / Sankaran, B. / Lorimer, D.D. / Myler, P.J. / Staker, B.L. / Stewart, L.J.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Oct 10, 2012Group: Non-polymer description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 2023Group: 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 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase-thymidylate synthase
B: Dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,16627
Polymers117,1642
Non-polymers5,00225
Water18,4651025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17870 Å2
ΔGint-37 kcal/mol
Surface area37780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.330, 83.830, 83.920
Angle α, β, γ (deg.)119.61, 102.04, 90.26
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase-thymidylate synthase


Mass: 58581.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Babesia bovis (eukaryote) / Gene: BBOV_II000780 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ASX7, thymidylate synthase

-
Non-polymers , 8 types, 1050 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-D16 / TOMUDEX / ZD1694 / Raltitrexed / Raltitrexed


Mass: 458.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22N4O6S / Comment: chemotherapy, inhibitor*YM
#5: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1025 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 CO-CRYSTALLIZATION DROP. PROTEIN SOLUTION: 20 MG/ML PROTEIN, 2.0MM DUMP, 2.0MM NADP, 5.0MM RALTITREXED, 0.5M SODIUM CHLORIDE, 0.025M HEPES, 5%(V/V) GLYCEROL, 2.0MM DITHIOTHREITOL. ...Details: 1:1 CO-CRYSTALLIZATION DROP. PROTEIN SOLUTION: 20 MG/ML PROTEIN, 2.0MM DUMP, 2.0MM NADP, 5.0MM RALTITREXED, 0.5M SODIUM CHLORIDE, 0.025M HEPES, 5%(V/V) GLYCEROL, 2.0MM DITHIOTHREITOL. CRYSTALLANT SOLUTION (HT INDEX E11): 0.02M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M HEPES, 22%(W/V) POLY(ACRYLIC ACID) SODIUM SALT 5100, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9974 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9974 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 108796 / % possible obs: 97.2 % / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Χ2: 1.118 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.8320.3542.439104891.17695.9
1.83-1.8620.298104421.14396.2
1.86-1.920.263105041.14696.3
1.9-1.9420.22104461.15196.3
1.94-1.9820.192105061.16296.6
1.98-2.0320.16104791.14496.6
2.03-2.0820.149105021.15796.9
2.08-2.1320.125106731.14896.8
2.13-2.220.107104671.12997
2.2-2.2720.099106671.197.3
2.27-2.3520.092105321.11897.3
2.35-2.4420.082105961.1597.4
2.44-2.5520.079106481.08797.5
2.55-2.6920.068106491.0797.6
2.69-2.8620.06105431.00597.8
2.86-3.0820.052106381.11597.8
3.08-3.3920.047106951.07497.7
3.39-3.881.90.04105761.01497.7
3.88-4.881.90.036106731.14498.2
4.88-5020.033108091.1399.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K2H

3k2h


Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2251 / WRfactor Rwork: 0.1854 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8507 / SU B: 5.113 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1335 / SU Rfree: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5573 5.1 %RANDOM
Rwork0.1935 ---
obs0.1956 104245 98.52 %-
all-108796 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.91 Å2 / Biso mean: 19.8103 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20.06 Å2-0.25 Å2
2--1.5 Å21.26 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7965 0 329 1025 9319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228655
X-RAY DIFFRACTIONr_bond_other_d0.0010.025775
X-RAY DIFFRACTIONr_angle_refined_deg1.7532.0111818
X-RAY DIFFRACTIONr_angle_other_deg0.982314021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94223.455385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.993151315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6861556
X-RAY DIFFRACTIONr_chiral_restr0.1060.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021802
X-RAY DIFFRACTIONr_mcbond_it0.7581.55045
X-RAY DIFFRACTIONr_mcbond_other0.2461.52007
X-RAY DIFFRACTIONr_mcangle_it1.29128210
X-RAY DIFFRACTIONr_scbond_it2.12933610
X-RAY DIFFRACTIONr_scangle_it3.2024.53601
LS refinement shellResolution: 1.788→1.834 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 364 -
Rwork0.242 6186 -
all-6550 -
obs--79.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8530.39420.19992.16940.67241.54770.02090.1988-0.1319-0.3310.04580.1230.13030.045-0.06670.1630.0294-0.06530.0908-0.02690.151622.733-39.343-52.148
20.7962-1.73720.7936.4087-7.26862.65310.0972-0.1243-0.4057-1.1766-0.3939-0.27990.82920.40560.29670.39440.12880.11160.30180.08960.345947.184-12.194-54.396
30.7428-0.0802-0.02160.9062-0.09550.5620.0087-0.1039-0.00320.1021-0.00690.006-0.00410.0419-0.00180.0193-0.004-0.00580.05250.01470.060429.639-8.272-22.873
40.9772-0.4372-0.32661.4190.31081.1946-0.0161-0.1026-0.10990.1142-0.02150.12950.0617-0.04930.03750.0556-0.0014-0.01030.04670.03060.093922.398-21.46-24.063
51.341-0.0644-0.92471.0778-0.12792.02080.00340.1864-0.1116-0.1442-0.1216-0.10790.17040.16440.11810.07090.036-0.01120.18320.03620.091451.8885.571-71.653
60.08060.9020.09268.6489-2.4755-0.8974-0.06140.24220.196-1.6245-0.01060.39350.50820.04440.0720.52590.0165-0.10830.24780.02260.218524.512-14.983-58.553
70.66730.05590.03410.6811-0.15430.92030.0028-0.02070.09280.0519-0.00720.0796-0.131-0.0230.00440.0222-0.0046-0.00360.03390.01090.077828.28613.333-36.135
81.02930.19590.22130.67610.09872.1221-0.01570.0050.19560.0414-0.00760.0341-0.23440.07180.02330.0681-0.0049-0.00230.05250.02780.099737.63620.24-45.769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 186
2X-RAY DIFFRACTION2A187 - 214
3X-RAY DIFFRACTION3A215 - 470
4X-RAY DIFFRACTION4A471 - 511
5X-RAY DIFFRACTION5B3 - 186
6X-RAY DIFFRACTION6B187 - 214
7X-RAY DIFFRACTION7B215 - 470
8X-RAY DIFFRACTION8B471 - 511

+
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