[English] 日本語
Yorodumi
- PDB-6o9a: Crystal structure of MqnA complexed with 3-hydroxybenzoic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o9a
TitleCrystal structure of MqnA complexed with 3-hydroxybenzoic acid
ComponentsChorismate dehydratase
KeywordsLYASE / Menaquinone biosynthesis
Function / homology
Function and homology information


chorismate dehydratase / hydro-lyase activity / menaquinone biosynthetic process
Similarity search - Function
Chorismate dehydratase / Menaquinone biosynthesis enzyme / Menaquinone biosynthesis / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-HYDROXYBENZOIC ACID / ACETATE ION / Chorismate dehydratase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.326 Å
AuthorsHicks, K.A. / Mahanta, N. / Naseem, S. / Fedoseyenko, D. / Begley, T.P. / Ealick, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DK067081 United States
CitationJournal: Biochemistry / Year: 2019
Title: Menaquinone Biosynthesis: Biochemical and Structural Studies of Chorismate Dehydratase.
Authors: Mahanta, N. / Hicks, K.A. / Naseem, S. / Zhang, Y. / Fedoseyenko, D. / Ealick, S.E. / Begley, T.P.
History
DepositionMar 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chorismate dehydratase
B: Chorismate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5896
Polymers69,1942
Non-polymers3944
Water1,15364
1
A: Chorismate dehydratase
hetero molecules

B: Chorismate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5896
Polymers69,1942
Non-polymers3944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area4220 Å2
ΔGint-11 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.102, 151.619, 75.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
DetailsTHE AUTHORS STATE THAT PISA INDICATES THAT MQNA IS DIMERIC, WHICH IS CONSISTENT WITH THE CALCULATED MOLECULAR WEIGHT FROM GEL FILTRATION. HOWEVER, BOTH 6O9A AND 2I6E, WHICH BELONG TO DIFFERENT SPACE GROUPS, DISPLAY A COMMON, CONSERVED HYDROPHILIC INTERFACE, WHICH GENERATES POTENTIAL TETRAMERS.

-
Components

#1: Protein Chorismate dehydratase / Menaquinone biosynthetic enzyme MqnA


Mass: 34597.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: mqnA, DR_0370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RXE3, chorismate dehydratase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-3HB / 3-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M acetate (pH 5.5), 13% PEG 1500, 2.5 M sodium chloride (NaCl), and 1.5% 2-methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 34973 / % possible obs: 98.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Χ2: 2.134 / Net I/σ(I): 20.5 / Num. measured all: 138300
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.32-2.3630.13416951.319197.4
2.36-2.43.30.1317351.341199.9
2.4-2.453.50.12617251.471199.8
2.45-2.53.70.12217421.465199.7
2.5-2.554.10.11717611.5951100
2.55-2.614.10.10417371.57199.8
2.61-2.684.10.09917581.736199.7
2.68-2.754.10.09317321.676199.9
2.75-2.834.10.08617501.769199.5
2.83-2.924.10.08117291.98199.5
2.92-3.034.10.07817542.089199.4
3.03-3.154.10.07517662.277199.4
3.15-3.294.10.07217432.402199.4
3.29-3.474.10.06817552.503199.2
3.47-3.684.10.06917452.907198.9
3.68-3.974.10.06817492.996198.4
3.97-4.374.10.06517603.075198.9
4.37-54.10.06517583.104197.9
5-6.294.10.06217802.7197.5
6.29-503.80.04717992.004194.5

-
Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I6E

2i6e


Resolution: 2.326→42.759 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 1759 5.03 %
Rwork0.1911 33204 -
obs0.1928 34963 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.26 Å2 / Biso mean: 31.2625 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 2.326→42.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4147 0 28 64 4239
Biso mean--33.73 27.6 -
Num. residues----542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3263-2.38920.27021270.2222400252795
2.3892-2.45950.25961170.209625562673100
2.4595-2.53890.31671340.223825702704100
2.5389-2.62960.27371260.219825502676100
2.6296-2.73490.26951530.225125662719100
2.7349-2.85940.24891230.224625552678100
2.8594-3.01010.23781430.21292544268799
3.0101-3.19860.26091570.213625462703100
3.1986-3.44550.22281380.19842574271299
3.4455-3.7920.21081500.18752537268799
3.792-4.34030.18631380.16432589272799
4.3403-5.46650.18721330.15222572270598
5.4665-42.76630.18881200.17712645276595

+
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://pdbjlc1.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