[English] 日本語
Yorodumi
- PDB-5wm7: Crystal Structure of CahJ in Complex with AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wm7
TitleCrystal Structure of CahJ in Complex with 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 / Salicylate-AMP ligase
Similarity search - Component
Biological speciesStreptomyces gandocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.777 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)61,2824
Polymers60,7841
Non-polymers4983
Water6,936385
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)121.916, 121.916, 87.996
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1006-

HOH

-
Components

#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
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 385 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
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 7, 2016
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: 0.53
ReflectionResolution: 1.777→45.27 Å / Num. obs: 70015 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 4.064 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.11 / Χ2: 0.989 / Net I/σ(I): 11.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.777-1.884.020.7771.76111020.4580.88395.1
1.88-2.014.1050.4863.03105990.7080.54996.6
2.01-2.183.9490.2825.1298950.880.31996.8
2.18-2.384.1770.1817.8791090.950.20496.3
2.38-2.664.0630.12710.8782350.9720.14396.3
2.66-3.074.1270.0816.6473190.9890.08996.9
3.07-3.764.0480.05125.4162550.9950.05796.8
3.76-5.34.0610.03833.3648050.9970.04395.6
5.3-45.274.0060.03834.0126940.9970.04392.3

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5WM2

5wm2


Resolution: 1.777→45.27 Å / Cross valid method: FREE R-VALUE / σ(F): 56.73 / Phase error: 20.1
RfactorNum. reflection% reflection
Rfree0.1737 1163 1.93 %
Rwork0.1356 --
obs0.1452 70015 96.125 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.13 Å2 / Biso mean: 21.3024 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.777→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 33 385 4466
Biso mean--20 32.09 -
Num. residues----535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064176
X-RAY DIFFRACTIONf_angle_d0.8515703
X-RAY DIFFRACTIONf_chiral_restr0.052647
X-RAY DIFFRACTIONf_plane_restr0.006759
X-RAY DIFFRACTIONf_dihedral_angle_d9.2783420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.779-1.82340.32131520.25718291844383
1.8234-1.87270.27241510.23498389854083
1.8727-1.92780.2591450.21998303844883
1.9278-1.99010.23711360.20018271840782
1.9901-2.06120.20281280.18628156828481
2.0612-2.14370.22081410.16978204834582
2.1437-2.24130.21951340.15888353848783
2.2413-2.35940.17571530.15468223837682
2.3594-2.50720.18281150.14538296841183
2.5072-2.70070.15811400.14898147828781
2.7007-2.97240.16271590.13598316847583
2.9724-3.40220.18261390.13378373851284
3.4022-4.28520.17461370.11198339847683
4.2852-35.6830.131360.10438286842282
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)
12.3158-0.9402-0.07580.85390.15551.59540.13710.0484-0.2038-0.21010.00050.06820.203-0.0498-0.11920.196-0.0446-0.03230.1874-0.03660.1151-13.50941.0392-13.3312
22.1060.65760.08981.16010.02560.85150.00150.0263-0.13940.08110.02-0.0320.11530.0414-0.00620.15810.01390.00330.12010.0080.12921.601433.37538.0028
30.8896-0.2275-0.34480.58890.10291.157-0.0399-0.0436-0.0544-0.00310.01290.02690.1137-0.10390.03050.1395-0.02780.00520.1560.01850.1105-17.218638.875614.8851
40.66970.12360.17050.4856-0.20010.7385-0.06310.0225-0.0626-0.04710.04740.00560.0935-0.03180.02640.1193-0.02080.01350.1307-0.01650.0838-7.909843.76740.8344
50.6526-0.3397-0.22921.52870.19430.4673-0.0271-0.04340.0010.06880.0075-0.05410.0208-0.00010.02170.1077-0.0048-0.00320.13450.00030.06962.452854.119211.8451
60.77480.10110.1150.61290.0560.6211-0.00890.0630.0467-0.0475-0.00030.0471-0.0216-0.06360.00970.1087-0.00880.00520.12460.0030.0625-8.119560.7275-3.8436
70.82060.0487-0.74050.1623-0.00990.75410.00980.06040.06010.02990.02080.0347-0.0269-0.1376-0.04070.14820.0112-0.00770.178-0.00810.1394-21.422865.93897.1917
80.20670.039-0.03890.2466-0.01730.1852-0.00630.00680.0668-0.00140.01220.0995-0.0676-0.08870.03770.1246-0.0066-0.00620.1592-0.01050.1007-19.668659.284810.1881
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 189 )A91 - 189
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 255 )A190 - 255
5X-RAY DIFFRACTION5chain 'A' and (resid 256 through 312 )A256 - 312
6X-RAY DIFFRACTION6chain 'A' and (resid 313 through 433 )A313 - 433
7X-RAY DIFFRACTION7chain 'A' and (resid 434 through 499 )A434 - 499
8X-RAY DIFFRACTION8chain 'A' and (resid 500 through 553 )A500 - 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