[English] 日本語
Yorodumi
- PDB-4rm2: Crystal structure of a benzoate coenzyme A ligase with 2-Fluoro b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rm2
TitleCrystal structure of a benzoate coenzyme A ligase with 2-Fluoro benzoic acid
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE / Substrate Specificity / Kinetics
Function / homology
Function and homology information


acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-fluorobenzoic acid / Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsStrom, S. / Nosrati, M. / Thornburg, C. / Walker, K.D. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2015
Title: Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity.
Authors: Thornburg, C.K. / Wortas-Strom, S. / Nosrati, M. / Geiger, J.H. / Walker, K.D.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 20, 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: Benzoate-coenzyme A ligase
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0885
Polymers112,6672
Non-polymers4203
Water13,295738
1
A: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6143
Polymers56,3341
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4742
Polymers56,3341
Non-polymers1401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.885, 95.749, 98.605
Angle α, β, γ (deg.)90.00, 110.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Benzoate-coenzyme A ligase


Mass: 56333.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: badA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q93TK0
#2: Chemical ChemComp-3U4 / 2-fluorobenzoic acid


Mass: 140.112 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5FO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 % PEG 3350, 0.1 M Tris pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 92681 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.105 / Rsym value: 0.083 / Net I/σ(I): 12.68
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.55 / Rsym value: 0.437 / % possible all: 80.81

-
Processing

Software
NameVersionClassification
HKL-2000data collection
molrepmodel building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
molrepphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V7B

2v7b


Resolution: 1.77→41.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.668 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20167 4931 5.1 %RANDOM
Rwork0.15913 ---
obs0.16127 92653 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7851 0 30 738 8619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198156
X-RAY DIFFRACTIONr_bond_other_d0.0010.027662
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.96911141
X-RAY DIFFRACTIONr_angle_other_deg0.943317614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59651053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70822.899338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.037151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.491558
X-RAY DIFFRACTIONr_chiral_restr0.1280.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021877
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_it1.8771.7664158
X-RAY DIFFRACTIONr_mcbond_other1.8761.7654157
X-RAY DIFFRACTIONr_mcangle_it2.6732.6395199
X-RAY DIFFRACTIONr_mcangle_other2.372.5225061
X-RAY DIFFRACTIONr_scbond_it2.6112.0123998
X-RAY DIFFRACTIONr_scbond_other2.5691.9663929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8752.845822
X-RAY DIFFRACTIONr_long_range_B_refined5.23214.4969391
X-RAY DIFFRACTIONr_long_range_B_other5.06314.1329058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 295 -
Rwork0.281 5612 -
obs--80.81 %

+
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