[English] 日本語
Yorodumi
- PDB-3mcv: Structure of PTR1 from Trypanosoma brucei in ternary complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mcv
TitleStructure of PTR1 from Trypanosoma brucei in ternary complex with 2,4-diamino-5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]-pyrimidine and NADP+
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Pteridine reductase / antifolate
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-MCV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsTulloch, L.B. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: High-resolution structures of Trypanosoma brucei pteridine reductase ligand complexes inform on the placement of new molecular entities in the active site of a potential drug target.
Authors: Dawson, A. / Tulloch, L.B. / Barrack, K.L. / Hunter, W.N.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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_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: Pteridine reductase
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,21116
Polymers122,6794
Non-polymers4,53112
Water14,286793
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20390 Å2
ΔGint-130 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.502, 89.819, 82.260
Angle α, β, γ (deg.)90.00, 115.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Pteridine reductase


Mass: 30669.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O76290, pteridine reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-MCV / 5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]pyrimidine-2,4-diamine


Mass: 330.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18N4O2S
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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: 2.03 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.8 M sodium acetate, 50 mM sodium citrate, 1mM DTT, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97857 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→40.761 Å / Num. all: 105672 / Num. obs: 105672 / % possible obs: 98.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.795.50.3082.483549152260.30897.4
1.79-1.95.50.2243.479813143830.22497.7
1.9-2.035.60.1425.376325136350.14298.1
2.03-2.195.70.0957.872551127570.09598.5
2.19-2.45.80.0710.167951117760.0798.8
2.4-2.695.80.06210.961622106540.06299.1
2.69-3.15.80.04812.45486694860.04899.3
3.1-3.85.80.03415.14634480240.03499.6
3.8-5.385.80.02520.43603262530.02599.7
5.38-44.95.60.02816.71954734780.02899.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.169 / WRfactor Rwork: 0.139 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.918 / SU B: 3.027 / SU ML: 0.052 / SU R Cruickshank DPI: 0.086 / SU Rfree: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.167 5310 5 %RANDOM
Rwork0.135 ---
obs0.137 105645 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.59 Å2 / Biso mean: 13.678 Å2 / Biso min: 2.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å2-0.61 Å2
2--1.7 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7453 0 300 793 8546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228082
X-RAY DIFFRACTIONr_bond_other_d0.0010.025202
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.00711068
X-RAY DIFFRACTIONr_angle_other_deg0.9353.00212771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68951056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10924.441313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.603151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3231549
X-RAY DIFFRACTIONr_chiral_restr0.0750.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021483
X-RAY DIFFRACTIONr_nbd_refined0.210.21766
X-RAY DIFFRACTIONr_nbd_other0.1920.25921
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24021
X-RAY DIFFRACTIONr_nbtor_other0.0860.24057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2668
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.225
X-RAY DIFFRACTIONr_mcbond_it2.17446589
X-RAY DIFFRACTIONr_mcbond_other0.53142057
X-RAY DIFFRACTIONr_mcangle_it2.47168188
X-RAY DIFFRACTIONr_scbond_it3.55583470
X-RAY DIFFRACTIONr_scangle_it4.728102845
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 358 -
Rwork0.158 7335 -
all-7693 -
obs--97.06 %
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)
10.4174-0.0760.01850.3498-0.04390.4535-0.00360.0551-0.015-0.0208-0.0041-0.01780.04030.11150.0076-0.02490.01470.005-0.01050.0022-0.018811.6123-4.87189.4246
20.4405-0.07020.09210.1525-0.00280.5706-0.0070.0661-0.0058-0.0119-0.01230.0182-0.0063-0.03420.0192-0.02050.0016-0.008-0.027-0.0025-0.0164-17.32283.3066-1.2597
30.41910.04830.02010.29250.0260.5113-0.0155-0.09440.02320.02940.0022-0.0102-0.01020.03770.0133-0.01780.0022-0.0041-0.0126-0.0045-0.02741.36735.061937.8441
40.4643-0.1390.02520.23210.04770.5063-0.0219-0.0785-0.05180.010.00470.0380.0334-0.11760.0172-0.0322-0.0110.0118-0.00210.0024-0.0063-27.6713-3.318527.9934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 268
2X-RAY DIFFRACTION2B2 - 268
3X-RAY DIFFRACTION3C2 - 268
4X-RAY DIFFRACTION4D2 - 268

+
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