[English] 日本語
Yorodumi
- PDB-2vz0: Pteridine Reductase 1 (PTR1) from Trypanosoma Brucei in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vz0
TitlePteridine Reductase 1 (PTR1) from Trypanosoma Brucei in complex with NADP and DDD00066641
ComponentsPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / TRYPANOSOMATIDS / PTERIDINE REDUCTASE
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
6-(4-methylphenyl)quinazoline-2,4-diamine / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRobinson, D.A. / Thompson, S. / Sienkiewicz, N. / Fairlamb, A.H.
Citation
Journal: Anal.Biochem. / Year: 2010
Title: Development and Validation of a Cytochrome C Coupled Assay for Pteridine Reductase 1 and Dihydrofolate Reductase.
Authors: Shanks, E.J. / Ong, H.B. / Robinson, D.A. / Thompson, S. / Sienkiewicz, N. / Fairlamb, A.H. / Frearson, J.A.
#1: Journal: Mol.Microbiol. / Year: 2006
Title: Structure and Reactivity of Trypanosoma Brucei Pteridine Reductase: Inhibition by the Archetypal Antifolate Methotrexate.
Authors: Dawson, A. / Gibellini, F. / Sienkiewicz, N. / Tulloch, L.B. / Fyfe, P.K. / Mcluskey, K. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionJul 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)117,96912
Polymers113,9944
Non-polymers3,9758
Water20,6451146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17780 Å2
ΔGint-167.8 kcal/mol
Surface area39870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.479, 90.822, 82.616
Angle α, β, γ (deg.)90.00, 115.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.77456, -0.04039, -0.6312), (-0.03055, -0.9944, 0.10113), (-0.63176, 0.09761, 0.769)-2.55488, -2.16944, -0.78833
2given(0.76873, 0.02395, 0.63912), (0.02161, -0.9997, 0.01147), (0.6392, 0.00499, -0.76902)-13.54485, -0.08137, 37.55108
3given(-0.99994, 0.01071, 0.00213), (0.01043, 0.99443, -0.10492), (-0.00324, -0.1049, -0.99448)-15.96963, 1.94596, 36.61332

-
Components

#1: Protein
PTERIDINE REDUCTASE / PTERIDINE REDUCTASE 1


Mass: 28498.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET-TBPTR1H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / 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-D64 / 6-(4-methylphenyl)quinazoline-2,4-diamine


Mass: 250.298 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1146 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details6-P-TOLYL-QUINAZOLINE-2,4-DIAMINE (D64): DDD00066641

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 6 / Details: 1.8M NA ACETATE, 0.1M CITRATE BUFFER PH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 17, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 72743 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / % possible all: 75.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7V

2c7v


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.662 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3654 5 %RANDOM
Rwork0.154 ---
obs0.156 69014 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-0.64 Å2
2--2.19 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7410 0 268 1146 8824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227817
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4442.00510659
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99324.286301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.846151233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1671548
X-RAY DIFFRACTIONr_chiral_restr0.0890.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025780
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.24431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.25407
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7261.55117
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08527918
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.80433170
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.64.52740
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 201
Rwork0.261 3754
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)
10.88270.06830.20860.82840.04450.8653-0.00850.0272-0.0239-0.0531-0.0244-0.06990.06570.12960.0329-0.10580.01740.0107-0.1161-0.0009-0.101711.6889-4.53729.3119
20.9066-0.05170.06050.5386-0.13350.8895-0.00680.0387-0.0132-0.0307-0.01510.04680.0211-0.05850.0219-0.105-0.00090.0007-0.12670.0014-0.1058-17.32563.0681-1.4172
31.24450.02330.11240.51830.25891.1098-0.0137-0.11880.05060.09080.0111-0.0141-0.02960.01880.0026-0.08460.0117-0.0016-0.0944-0.0098-0.10891.25824.89237.8669
41.2531-0.13990.10050.33350.02881.1108-0.0269-0.1011-0.09280.05260.00950.05840.082-0.11340.0174-0.0925-0.01170.0195-0.07070.0111-0.0785-27.7122-3.450927.7978
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