[English] 日本語
Yorodumi
- PDB-6f9p: Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f9p
TitleCrystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Re(II)
ComponentsL-lysine 4-hydroxylase
KeywordsOXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII alphaKG form / oxydoreductase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding
Similarity search - Function
Clavaminate synthase-like / Double-stranded beta-helix / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RHENIUM / L-lysine 4-hydroxylase
Similarity search - Component
Biological speciesFlavobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsIsabet, T. / Stura, E. / Legrand, P. / Zaparucha, A. / Bastard, K.
CitationJournal: Sci Rep / Year: 2018
Title: Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.
Authors: Bastard, K. / Isabet, T. / Stura, E.A. / Legrand, P. / Zaparucha, A.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-lysine 4-hydroxylase
B: L-lysine 4-hydroxylase
C: L-lysine 4-hydroxylase
D: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,53516
Polymers167,2694
Non-polymers1,26712
Water3,045169
1
A: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2315
Polymers41,8171
Non-polymers4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0393
Polymers41,8171
Non-polymers2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0393
Polymers41,8171
Non-polymers2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2275
Polymers41,8171
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.200, 98.870, 165.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
L-lysine 4-hydroxylase / Alpha-ketoglutarate-dependent dioxygenase / KDO5 / L-lysine hydroxylase


Mass: 41817.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. (strain CF136) (bacteria)
Strain: CF136 / Gene: PMI10_03368 / Production host: Escherichia coli (E. coli)
References: UniProt: J3BZS6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

-
Non-polymers , 5 types, 181 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-RE / RHENIUM


Mass: 186.207 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Re
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 % PEG 4000, 0.2M Imidazole malate PH 7.0, 0.15M LI2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1761 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1761 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 58758 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 67.98 Å2 / Rrim(I) all: 0.125 / Net I/σ(I): 15.15
Reflection shellResolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.2 / Rrim(I) all: 1.662 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PARROTphasing
XSCALEdata scaling
BUCCANEERmodel building
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.43 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.367 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2925 4.98 %RANDOM
Rwork0.194 ---
obs0.195 58757 100 %-
Displacement parametersBiso mean: 83.81 Å2
Baniso -1Baniso -2Baniso -3
1--13.265 Å20 Å20 Å2
2---5.5538 Å20 Å2
3---18.8188 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.4→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10407 0 29 169 10605
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110698HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1114472HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3703SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes290HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1541HARMONIC5
X-RAY DIFFRACTIONt_it10698HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion17.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1380SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12150SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2764 212 4.95 %
Rwork0.2479 4071 -
all0.2493 4283 -
obs--99.88 %
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)
11.1143-0.4381-0.26811.68070.1661.80370.0174-0.1390.02780.17950.0629-0.07120.16550.1292-0.08030.019-0.0425-0.0562-0.1608-0.0002-0.2074-0.049861.004633.8617
21.4490.348-0.15681.86650.85492.21820.02340.12960.1331-0.58780.0526-0.0356-0.7722-0.0966-0.07610.33610.02750.0511-0.24270.07-0.2317-0.674577.76852.3347
31.6137-0.1258-0.02161.90730.65022.98040.105-0.041-0.2190.63320.03870.07521.1578-0.0435-0.14370.67-0.0217-0.0503-0.14570.0154-0.1328-0.118523.1077-1.7944
42.5820.70630.75551.95260.73222.65090.00690.74450.0253-0.27250.2079-0.1007-0.09960.5158-0.21480.0490.01740.06010.20940.0039-0.16864.399738.8912-33.4636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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