[English] 日本語
Yorodumi
- PDB-5wm2: Crystal Structure of CahJ in Complex with Salicylic Acid and AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wm2
TitleCrystal Structure of CahJ in Complex with Salicylic Acid and AMP
ComponentsSalicylate-AMP ligase
KeywordsLIGASE / Adenylation Domain / Peptide Synthetase
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds
Similarity search - Function
ANL, C-terminal domain / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...ANL, C-terminal domain / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / 2-HYDROXYBENZOIC ACID / Salicylate-AMP ligase
Similarity search - Component
Biological speciesStreptomyces gandocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.548 Å
AuthorsSikkema, A.P. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118101 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008270 United States
CitationJournal: Chembiochem / Year: 2018
Title: A Defined and Flexible Pocket Explains Aryl Substrate Promiscuity of the Cahuitamycin Starter Unit-Activating Enzyme CahJ.
Authors: Tripathi, A. / Park, S.R. / Sikkema, A.P. / Cho, H.J. / Wu, J. / Lee, B. / Xi, C. / Smith, J.L. / Sherman, D.H.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Salicylate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5126
Polymers60,7841
Non-polymers7295
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.872, 121.872, 87.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Salicylate-AMP ligase


Mass: 60783.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces gandocaensis (bacteria) / Gene: cahJ / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A140DJY3

-
Non-polymers , 5 types, 529 molecules

#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Sodium Cacodylate pH 6.5, 1.7 M Sodium Acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.46
ReflectionResolution: 1.548→45.215 Å / Num. obs: 109137 / % possible obs: 99.925 % / Observed criterion σ(I): -3 / Redundancy: 10.016 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Χ2: 0.985 / Net I/σ(I): 20.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.548-1.649.7070.9552.43173960.6371.00999.6
1.64-1.7510.0450.5974.1164720.8460.629100
1.75-1.8910.1490.337.34153770.9460.348100
1.89-2.089.8750.17813.15141800.9820.188100
2.08-2.3210.3480.10522.15128270.9930.111100
2.32-2.689.9380.07230.6113700.9960.076100
2.68-3.2810.40.04845.4996560.9980.051100
3.28-4.629.8870.03562.3275340.9990.037100
4.62-45.2159.7130.03565.6843250.9990.03799.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MD9

1md9


Resolution: 1.548→45.215 Å / Cross valid method: FREE R-VALUE / σ(F): 54.79 / Phase error: 14.97
RfactorNum. reflection% reflection
Rfree0.1585 1805 1.65 %
Rwork0.1255 --
obs0.1475 109137 99.925 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.73 Å2 / Biso mean: 19.8281 Å2 / Biso min: 8.15 Å2
Refinement stepCycle: final / Resolution: 1.548→45.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 49 524 4629
Biso mean--23.79 30.88 -
Num. residues----536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064290
X-RAY DIFFRACTIONf_angle_d0.8235877
X-RAY DIFFRACTIONf_chiral_restr0.052666
X-RAY DIFFRACTIONf_plane_restr0.006788
X-RAY DIFFRACTIONf_dihedral_angle_d10.3993474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5485-1.57520.26321810.25781039810579
1.5752-1.60390.27821760.23661042010596
1.6039-1.63470.26731800.22241037910559
1.6347-1.66810.22391820.2071052910711
1.6681-1.70440.20711660.19321043010596
1.7044-1.7440.23881740.18011040210576
1.744-1.78760.15851700.16121043210602
1.7876-1.8360.19961840.15751040610590
1.836-1.890.18721740.1491041610590
1.89-1.9510.1561780.15131043410612
1.951-2.02070.15681640.14541039610560
2.0207-2.10160.14131680.15021046910637
2.1016-2.19720.17361780.15171045410632
2.1972-2.3130.17381740.1481041210586
2.313-2.45790.17971700.14561046610636
2.4579-2.64770.19291690.14581038810557
2.6477-2.9140.15851900.13991042410614
2.914-3.33540.17661700.14091044310613
3.3354-4.20120.17731760.13291041810594
4.2012-35.59860.161810.11651043410615
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)
12.6701-1.743-0.41661.14070.34112.94210.07150.1179-0.1974-0.1725-0.01590.10330.2134-0.0866-0.03320.1881-0.0487-0.03350.1797-0.04110.1086-13.541441.2066-13.324
23.42930.89160.2011.58270.2291.7472-0.01350.0275-0.24120.02390.0254-0.0740.09180.0493-0.00240.13240.01590.00580.1006-0.00380.11011.476233.37897.9395
30.6785-0.1167-0.21740.5892-0.13361.2164-0.037-0.0346-0.0809-0.01130.01030.02350.1203-0.09770.02860.1324-0.03930.01050.1556-0.0010.1121-16.922438.698112.1059
40.40380.08470.06110.76860.1620.6147-0.0035-0.0068-0.02390.02140.0056-0.04780.01420.0108-0.00270.1067-0.00730.00360.1341-0.00490.06960.623955.05656.4476
51.25130.53540.0760.92860.02270.5421-0.03490.1150.0809-0.0970.04030.131-0.0235-0.1116-0.00270.1297-0.002-0.01530.16860.0060.0732-13.92661.6018-7.8814
61.26050.1453-0.1091.1645-0.27650.79120.0073-0.06410.05480.07260.00290.1579-0.0065-0.1049-0.02440.12620.00020.01310.176-0.020.105-28.42164.453316.5907
71.51690.0051-0.1592.8737-0.04412.0752-0.05320.20970.278-0.16050.0460.2683-0.2972-0.2126-0.01280.1770.004-0.01260.2330.02460.1847-29.220271.407710.7323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 46 )A19 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 90 )A47 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 218 )A91 - 218
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 360 )A219 - 360
5X-RAY DIFFRACTION5chain 'A' and (resid 361 through 458 )A361 - 458
6X-RAY DIFFRACTION6chain 'A' and (resid 459 through 518 )A459 - 518
7X-RAY DIFFRACTION7chain 'A' and (resid 519 through 554 )A519 - 554

+
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