[English] 日本語
Yorodumi
- PDB-7a9j: Crystal structure of the R395G mutant form of Coronafacic Acid Li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a9j
TitleCrystal structure of the R395G mutant form of Coronafacic Acid Ligase from Pectobacterium brasiliense
ComponentsCfl
KeywordsLIGASE
Function / homology
Function and homology information


medium-chain fatty acid-CoA ligase activity / fatty acid metabolic process
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / 6-ethyl-1-oxidanylidene-indene-4-carboxylic acid / Cfl
Similarity search - Component
Biological speciesPectobacterium brasiliense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K002341/1 United Kingdom
Citation
Journal: Nature / Year: 2021
Title: Discovery, characterization and engineering of ligases for amide synthesis.
Authors: Winn, M. / Rowlinson, M. / Wang, F. / Bering, L. / Francis, D. / Levy, C. / Micklefield, J.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionSep 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
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 1, 2024Group: 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: Cfl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6984
Polymers60,3061
Non-polymers3923
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-13 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.611, 115.167, 71.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-917-

HOH

-
Components

#1: Protein Cfl / Ligase


Mass: 60306.312 Da / Num. of mol.: 1 / Mutation: R395G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium brasiliense (bacteria) / Gene: cfl, KCO_08370, KU74_07105 / Production host: Escherichia coli (E. coli) / References: UniProt: M4GWN4
#2: Chemical ChemComp-R4Z / 6-ethyl-1-oxidanylidene-indene-4-carboxylic acid


Mass: 202.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium sulfate, 0.05M magnesium sulphate heptahydrate, 0.1M Bicine pH 9, 20% v/v PEG smear medium
Temp details: Cold room

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.72→71.01 Å / Num. obs: 68261 / % possible obs: 99.82 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Net I/σ(I): 9.48
Reflection shellResolution: 1.72→1.781 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 6717 / CC1/2: 0.785 / CC star: 0.938 / Rpim(I) all: 0.5328 / % possible all: 99.35

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse

Resolution: 1.72→71.01 Å / SU ML: 0.1654 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 3297 4.83 %
Rwork0.1724 64911 -
obs0.1741 68208 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.19 Å2
Refinement stepCycle: LAST / Resolution: 1.72→71.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4003 0 25 323 4351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01494155
X-RAY DIFFRACTIONf_angle_d1.30315642
X-RAY DIFFRACTIONf_chiral_restr0.0919639
X-RAY DIFFRACTIONf_plane_restr0.0093715
X-RAY DIFFRACTIONf_dihedral_angle_d21.1511533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.30041170.30182623X-RAY DIFFRACTION96.92
1.74-1.770.31081420.28052647X-RAY DIFFRACTION99.79
1.77-1.80.25181340.25232650X-RAY DIFFRACTION99.54
1.8-1.830.26671490.2382682X-RAY DIFFRACTION99.86
1.83-1.860.24861450.22192670X-RAY DIFFRACTION99.65
1.86-1.890.21211240.21082662X-RAY DIFFRACTION99.93
1.89-1.930.2491170.19672707X-RAY DIFFRACTION99.72
1.93-1.970.21731270.18752675X-RAY DIFFRACTION99.89
1.97-2.010.19141440.17862672X-RAY DIFFRACTION99.86
2.01-2.060.21231210.17162715X-RAY DIFFRACTION99.86
2.06-2.110.20171360.17492680X-RAY DIFFRACTION99.89
2.11-2.170.20561300.16842699X-RAY DIFFRACTION99.96
2.17-2.230.21061170.16612720X-RAY DIFFRACTION99.93
2.23-2.30.19491360.16942678X-RAY DIFFRACTION99.89
2.3-2.380.22041430.1682690X-RAY DIFFRACTION99.96
2.38-2.480.21451430.17472698X-RAY DIFFRACTION99.89
2.48-2.590.23431670.17892671X-RAY DIFFRACTION100
2.59-2.730.21681600.1722715X-RAY DIFFRACTION99.9
2.73-2.90.21911460.17982705X-RAY DIFFRACTION100
2.9-3.120.2391310.18452732X-RAY DIFFRACTION99.97
3.12-3.440.24161450.17332736X-RAY DIFFRACTION100
3.44-3.940.1811320.15792777X-RAY DIFFRACTION100
3.94-4.960.15551470.13862786X-RAY DIFFRACTION100
4.96-71.010.21391440.182921X-RAY DIFFRACTION99.42
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)
12.342612915090.377007525522-0.3858950432461.66957261886-0.05688187217032.143746244050.0393487717315-0.128893523817-0.42592020340.205172363484-0.06723616815610.06680952609620.451167883144-0.166996864030.02064827771170.270798814721-0.0411744991447-0.02205384937150.209385746120.02761032576130.24308868810567.877555408825.625754923560.9822111133
21.893874692490.498154919534-0.4822371756641.77708926109-0.6353390086332.376146936540.0003217077695070.2127977162120.0763580467132-0.1447952623340.1029020562790.157112638797-0.0697409721606-0.15871573319-0.1104237649680.180669605974-0.0398522724758-0.01425656564210.228464413418-0.002661142411850.20637104506670.804667551744.157422938943.9334535974
33.793106056391.101324981072.429121120351.667556658190.3810282866253.04835444991-0.4463870378590.02400079626430.861316157459-0.03788063533020.1577896755670.393777042582-0.6344338897820.1148523676320.2177795102010.478694181175-0.0744448002166-0.03661669301510.34019086977-0.0222317723140.47246835115459.983526777447.910260870318.8266128196
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 197 )22 - 19723 - 194
22chain 'A' and (resid 198 through 397 )198 - 397195 - 394
33chain 'A' and (resid 398 through 537 )398 - 516395 - 509

+
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