[English] 日本語
Yorodumi
- PDB-2dtt: Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dtt
TitleCrystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 complexed with (1'R,2'S)-biopterin
ComponentsHypothetical protein PH0634
KeywordsLYASE / 6-pyruvoyl tetrahydrobiopterin synthase (PTPS) / Biopterin / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
6-pyruvoyl tetrahydropterin synthase/QueD / 6-pyruvoyl tetrahydropterin synthase/QueD family / 6-pyruvoyl tetrahydropterin synthase/QueD superfamily / 6-pyruvoyl tetrahydropterin synthase / Tetrahydropterin Synthase; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5,6,7,8-TETRAHYDROBIOPTERIN / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionJul 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hypothetical protein PH0634
B: Hypothetical protein PH0634
C: Hypothetical protein PH0634
D: Hypothetical protein PH0634
E: Hypothetical protein PH0634
F: Hypothetical protein PH0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,64212
Polymers81,1956
Non-polymers1,4476
Water7,296405
1
A: Hypothetical protein PH0634
B: Hypothetical protein PH0634
C: Hypothetical protein PH0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3216
Polymers40,5973
Non-polymers7243
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-6 kcal/mol
Surface area15300 Å2
MethodPISA
2
D: Hypothetical protein PH0634
E: Hypothetical protein PH0634
F: Hypothetical protein PH0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3216
Polymers40,5973
Non-polymers7243
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-3 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.682, 105.445, 96.147
Angle α, β, γ (deg.)90.00, 90.95, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a trimer. In the assymmetric unit subunits (A,B,C) and (D,E,F) represent biological units

-
Components

#1: Protein
Hypothetical protein PH0634 / 6-pyruvoyl tetrahydrobiopterin synthase


Mass: 13532.464 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0634 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O58368
#2: Chemical
ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: microbathch / pH: 6.25
Details: 16.5% PEG 20000, 0.1M Acetate, NAOH pH6.25, 3mM Biopterin, microbathch, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 21, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 36076 / Num. obs: 32611 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.067 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2906 / Rsym value: 0.225 / % possible all: 81.4

-
Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DJ6

2dj6


Resolution: 2.2→35.68 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1637 -RANDOM
Rwork0.195 ---
obs0.195 32611 90.4 %-
all-36076 --
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å2-6.17 Å2
2--2.24 Å20 Å2
3----5.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5403 0 102 405 5910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.65
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.272 131 -
Rwork0.231 --
obs-2851 79.4 %

+
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