[English] 日本語
Yorodumi
- PDB-2pg8: Crystal structure of R254K mutanat of DpgC with bound substrate analog -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pg8
TitleCrystal structure of R254K mutanat of DpgC with bound substrate analog
ComponentsDpgC
KeywordsLIGAND BINDING PROTEIN / Protein-ligand complex
Function / homology
Function and homology information


(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid beta-oxidation / antibiotic biosynthetic process / identical protein binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1300 / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1300 / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OXYGEN MOLECULE / Chem-YE1 / (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
Similarity search - Component
Biological speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFielding, E.N.
Citation
Journal: Biochemistry / Year: 2007
Title: Substrate Recognition and Catalysis by the Cofactor-Independent Dioxygenase DpgC.
Authors: Fielding, E.N. / Widboom, P.F. / Bruner, S.D.
#1: Journal: To be Published
Title: Structural Basis of cofactor independent dioxygenation in vancomycin biosynthesis
Authors: Widboom, P.F. / Fielding, E.N. / Liu, Y. / Bruner, S.D.
History
DepositionApr 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DpgC
B: DpgC
C: DpgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7348
Polymers137,9693
Non-polymers2,7665
Water2,216123
1
A: DpgC
B: DpgC
C: DpgC
hetero molecules

A: DpgC
B: DpgC
C: DpgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,46916
Polymers275,9376
Non-polymers5,53210
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area27410 Å2
ΔGint-79 kcal/mol
Surface area89640 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)139.054, 155.309, 169.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein DpgC


Mass: 45989.508 Da / Num. of mol.: 3 / Mutation: R254K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Strain: NRRL 15009 / Gene: DpgC / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21) / References: UniProt: Q8KLK7
#2: Chemical ChemComp-YE1 / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE


Mass: 900.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H43N8O19P3
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4000, 0.1M sodium citrate, 0.15M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2007 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 73908 / Num. obs: 73630 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.158 / Χ2: 1.899 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.749 / Num. unique all: 7244 / Χ2: 0.981 / % possible all: 99.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NP9

2np9


Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.367 7013 6.2 %random
Rwork0.331 ---
obs-69142 61.2 %-
Solvent computationBsol: 28.746 Å2
Displacement parametersBiso mean: 44.724 Å2
Baniso -1Baniso -2Baniso -3
1-6.795 Å20 Å20 Å2
2--23.497 Å20 Å2
3----30.292 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9619 0 181 123 9923
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0091.5
X-RAY DIFFRACTIONc_scbond_it1.3462
X-RAY DIFFRACTIONc_mcangle_it1.7642
X-RAY DIFFRACTIONc_scangle_it2.1372.5
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.421 770 -
Rwork0.383 --
obs-7527 82.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3YE1_o2.param

+
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