[English] 日本語
Yorodumi
- PDB-3orf: Crystal Structure of Dihydropteridine Reductase from Dictyosteliu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3orf
TitleCrystal Structure of Dihydropteridine Reductase from Dictyostelium discoideum
ComponentsDihydropteridine reductase
KeywordsOXIDOREDUCTASE / Alpha-Beta-Alpha Sandwich / Rossmann Fold / OXIDOREDUCTASE (acting on NADH) / NADH binding
Function / homology
Function and homology information


Phenylalanine metabolism / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / NADPH binding / phagocytic vesicle / NAD binding / response to oxidative stress ...Phenylalanine metabolism / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / NADPH binding / phagocytic vesicle / NAD binding / response to oxidative stress / identical protein binding / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydropteridine reductase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsChen, C. / Zhuang, N.N. / Seo, K.H. / Park, Y.S. / Lee, K.H.
CitationJournal: Febs Lett. / Year: 2011
Title: Structural insights into the dual substrate specificities of mammalian and Dictyostelium dihydropteridine reductases toward two stereoisomers of quinonoid dihydrobiopterin
Authors: Chen, C. / Kim, H.L. / Zhuang, N. / Seo, K.H. / Park, K.H. / Han, C.-D. / Park, Y.S. / Lee, K.H.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Nov 1, 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_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_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Dihydropteridine reductase
B: Dihydropteridine reductase
C: Dihydropteridine reductase
D: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0508
Polymers107,3964
Non-polymers2,6544
Water2,612145
1
A: Dihydropteridine reductase
B: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0254
Polymers53,6982
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area19000 Å2
MethodPISA
2
C: Dihydropteridine reductase
D: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0254
Polymers53,6982
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-20 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.808, 129.898, 78.763
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 2 - 231 / Label seq-ID: 22 - 251

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Dihydropteridine reductase / Quinoid dihydropteridine reductase


Mass: 26849.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0272684, qdpr / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86A17, 6,7-dihydropteridine reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17% PEG 3350, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 2.16 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.16 Å / Relative weight: 1
ReflectionResolution: 2.16→37 Å / Num. all: 50235 / Num. obs: 46917 / % possible obs: 93.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.081
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.423 / Num. unique all: 50235 / Rsym value: 0.081 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DHR

1dhr


Resolution: 2.16→36.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.783 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24014 2473 5 %RANDOM
Rwork0.18496 ---
obs0.18771 46917 93.57 %-
all-50235 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.939 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.16→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 176 145 7229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227232
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.989816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67825.373268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.963151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3411516
X-RAY DIFFRACTIONr_chiral_restr0.1390.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215288
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0741.54540
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85727268
X-RAY DIFFRACTIONr_scbond_it3.13632692
X-RAY DIFFRACTIONr_scangle_it4.8674.52548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1727 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.75
2Bloose positional0.495
3Cloose positional0.645
4Dloose positional0.525
1Aloose thermal3.8510
2Bloose thermal4.6910
3Cloose thermal4.4310
4Dloose thermal3.6410
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 171 -
Rwork0.281 3058 -
obs-46917 83.74 %
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)
10.5598-0.6233-0.31322.7306-0.14330.4096-0.07080.06790.14310.25690.0972-0.29130.03-0.09-0.02640.06740.0032-0.0770.07290.00260.133313.4284-9.44111.9007
20.4155-1.019-0.50372.51821.31941.41920.39080.07910.2079-0.8537-0.2048-0.5196-0.0895-0.1935-0.1860.46530.04190.20260.120.0760.123418.6517-16.9591-18.1776
30.79360.29180.46781.04390.2810.3146-0.07580.0038-0.0903-0.14670.08780.143-0.0632-0.0044-0.0120.0465-0.0360.02120.1252-0.02590.1254-0.1781-43.46189.4604
40.46370.20040.78211.00480.2532.05380.08180.0251-0.14910.24750.1573-0.20570.10330.1587-0.23920.08930.0405-0.01620.1202-0.0190.140318.4918-44.975634.9267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 231
2X-RAY DIFFRACTION2B2 - 231
3X-RAY DIFFRACTION3C2 - 231
4X-RAY DIFFRACTION4D2 - 231

+
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