[English] 日本語
Yorodumi
- PDB-2qw0: 4-Chlorobenzoyl-CoA Ligase/Synthetase, I303A mutation, bound to 3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qw0
Title4-Chlorobenzoyl-CoA Ligase/Synthetase, I303A mutation, bound to 3,4 Dichlorobenzoate
Components4-Chlorobenzoate CoA Ligase
KeywordsLIGASE / Adenylate-forming enzymes / Acyl-CoA ligase
Function / homology
Function and homology information


ligase activity / nucleotide binding / membrane / metal ion binding
Similarity search - Function
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-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase ...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-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3,4-dichlorobenzoate / 4-chlorobenzoyl CoA ligase
Similarity search - Component
Biological speciesAlcaligenes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsWu, R. / Reger, A.S. / Cao, J. / Gulick, A.M. / Dunaway-Mariano, D.
CitationJournal: Biochemistry / Year: 2007
Title: Rational redesign of the 4-chlorobenzoate binding site of 4-chlorobenzoate: coenzyme a ligase for expanded substrate range.
Authors: Wu, R. / Reger, A.S. / Cao, J. / Gulick, A.M. / Dunaway-Mariano, D.
History
DepositionAug 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AUTHOR MENTIONED THAT THE SEQUENCE USED IN THIS ENTRY MATCHES THE GB ACCESSION CODE ...SEQUENCE THE AUTHOR MENTIONED THAT THE SEQUENCE USED IN THIS ENTRY MATCHES THE GB ACCESSION CODE AAN10109 AND IS MUTATED AT RESIDUE 303 (I303A).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: 4-Chlorobenzoate CoA Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5302
Polymers54,3391
Non-polymers1911
Water1,928107
1
X: 4-Chlorobenzoate CoA Ligase
hetero molecules

X: 4-Chlorobenzoate CoA Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0604
Polymers108,6782
Non-polymers3822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)128.083, 128.083, 71.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein 4-Chlorobenzoate CoA Ligase


Mass: 54339.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes sp. (bacteria) / Strain: AL3007 / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8GN86*PLUS, EC: 6.2.1.33
#2: Chemical ChemComp-34Z / 3,4-dichlorobenzoate


Mass: 191.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4Cl2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 14-22% pentaerythritol propoxylate 426, 50 mM BTP, 1 mM ATP, 1 mM 3,4-DCB, pH 6.5-6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. obs: 20405 / % possible obs: 90.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.5
Reflection shellResolution: 2.56→2.63 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5D

1t5d


Resolution: 2.56→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 19.038 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25306 1075 5 %RANDOM
Rwork0.18508 ---
obs0.18837 20405 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.56→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 11 107 3861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223823
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.975206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44822.938160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31815598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5371536
X-RAY DIFFRACTIONr_chiral_restr0.1040.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022911
X-RAY DIFFRACTIONr_nbd_refined0.2110.21725
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.29
X-RAY DIFFRACTIONr_mcbond_it2.25822539
X-RAY DIFFRACTIONr_mcangle_it3.47733970
X-RAY DIFFRACTIONr_scbond_it2.58821421
X-RAY DIFFRACTIONr_scangle_it3.73131236
LS refinement shellResolution: 2.56→2.629 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 68 -
Rwork0.283 1222 -
obs--98.32 %
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)
12.8205-1.5088-1.06031.87881.01561.64620.0881-0.45550.188-0.29490.0959-0.34990.00650.4926-0.184-0.20990.03870.1095-0.0239-0.0016-0.0935-7.8436-47.0167-1.1747
23.1592-1.2238-1.0196.8916-0.35435.00430.57950.21540.1179-0.4333-0.3512-0.3627-0.7788-0.342-0.22830.14570.12290.2066-0.005-0.0124-0.1362-0.0794-62.0377-28.3257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA1 - 4021 - 402
2X-RAY DIFFRACTION2XA403 - 502403 - 502

+
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