[English] 日本語
Yorodumi
- PDB-4gqn: Crystallographic structure of trimeric Riboflavin Synthase from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gqn
TitleCrystallographic structure of trimeric Riboflavin Synthase from Brucella abortus in complex with 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione
ComponentsRiboflavin synthase subunit alpha
KeywordsTRANSFERASE / beta barrel / alpha + beta protein / riboflavin biosynthesis
Function / homologyElongation Factor Tu (Ef-tu); domain 3 - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta / Chem-INI / :
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSerer, M.I. / Bonomi, H.R. / Guimaraes, B.G. / Rossi, R.C. / Goldbaum, F.A. / Klinke, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility.
Authors: Serer, M.I. / Bonomi, H.R. / Guimaraes, B.G. / Rossi, R.C. / Goldbaum, F.A. / Klinke, S.
History
DepositionAug 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Sep 13, 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Riboflavin synthase subunit alpha
B: Riboflavin synthase subunit alpha
C: Riboflavin synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7989
Polymers69,9613
Non-polymers1,8376
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-44 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.850, 92.300, 99.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Riboflavin synthase subunit alpha


Mass: 23320.361 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: BAA13334_I02741, RIBE / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G8SX20, riboflavin synthase
#2: Chemical
ChemComp-INI / 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 306.229 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N4O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG 8000, 10% GLYCEROL, 0.5 M POTASSIUM CHLORIDE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 55235 / Num. obs: 55235 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.81 % / Biso Wilson estimate: 28.68 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 15.65
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.99 / Num. unique all: 8736 / Rsym value: 0.773 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4E0F

4e0f


Resolution: 1.85→27.09 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.9237 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 2765 5.01 %RANDOM
Rwork0.1999 ---
all0.2016 55210 --
obs0.2016 55210 99.73 %-
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.1766 Å20 Å20 Å2
2---3.5759 Å20 Å2
3----1.6007 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: LAST / Resolution: 1.85→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 126 307 5070
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074836HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.996558HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1698SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes766HARMONIC5
X-RAY DIFFRACTIONt_it4836HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion17.12
X-RAY DIFFRACTIONt_chiral_improper_torsion644SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5608SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2298 201 5.05 %
Rwork0.2169 3780 -
all0.2175 3981 -
obs-3981 99.73 %

+
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