[English] 日本語
Yorodumi
- PDB-4zav: UbiX in complex with a covalent adduct between dimethylallyl mono... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zav
TitleUbiX in complex with a covalent adduct between dimethylallyl monophosphate and reduced FMN
ComponentsUbiX
KeywordsLYASE / prenyl transferase / UbiX / FMN binding
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / carboxy-lyase activity / prenyltransferase activity
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4LS / PHOSPHATE ION / THIOCYANATE ION / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWhite, M.D. / Leys, D.
CitationJournal: Nature / Year: 2015
Title: UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis.
Authors: White, M.D. / Payne, K.A. / Fisher, K. / Marshall, S.A. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Rigby, S.E. / Scrutton, N.S. / Hay, S. / Leys, D.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UbiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2628
Polymers22,3851
Non-polymers8777
Water3,495194
1
A: UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)279,13896
Polymers268,61712
Non-polymers10,52184
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area76300 Å2
ΔGint-542 kcal/mol
Surface area68700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.180, 142.180, 142.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

21A-539-

HOH

31A-550-

HOH

41A-555-

HOH

51A-572-

HOH

61A-592-

HOH

71A-593-

HOH

81A-594-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein UbiX


Mass: 22384.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4019 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HX08, Lyases; Carbon-carbon lyases; Carboxy-lyases

-
Non-polymers , 5 types, 201 molecules

#2: Chemical ChemComp-4LS / 1-deoxy-1-[7,8-dimethyl-5-(3-methylbut-2-en-1-yl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono -D-ribitol / dimethylallyl FMN


Mass: 526.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H31N4O9P
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 3350, 150mM sodium thiocyanate, and 100mM Tris pH 7.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50.27 Å / Num. obs: 44084 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rpim(I) all: 0.027 / Net I/σ(I): 16
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 6.8 % / Rpim(I) all: 0.297 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→50.27 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.409 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.129 2399 5.2 %RANDOM
Rwork0.09769 ---
obs0.09927 44084 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.274 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.4→50.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 54 194 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021718
X-RAY DIFFRACTIONr_bond_other_d0.0060.021655
X-RAY DIFFRACTIONr_angle_refined_deg1.9832.0012350
X-RAY DIFFRACTIONr_angle_other_deg1.0673.0063804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2242465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48415272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0121512
X-RAY DIFFRACTIONr_chiral_restr0.4890.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211984
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02374
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_it2.2821.503880
X-RAY DIFFRACTIONr_mcbond_other2.2871.506881
X-RAY DIFFRACTIONr_mcangle_it2.7452.2411109
X-RAY DIFFRACTIONr_mcangle_other2.7442.2441110
X-RAY DIFFRACTIONr_scbond_it4.1961.869837
X-RAY DIFFRACTIONr_scbond_other4.1861.861832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8952.6671238
X-RAY DIFFRACTIONr_long_range_B_refined6.55714.1722042
X-RAY DIFFRACTIONr_long_range_B_other6.55714.1842043
X-RAY DIFFRACTIONr_rigid_bond_restr5.48733372
X-RAY DIFFRACTIONr_sphericity_free27.389547
X-RAY DIFFRACTIONr_sphericity_bonded13.84653483
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 182 -
Rwork0.181 3285 -
obs--100 %

+
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