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- PDB-5wm5: Crystal Structure of CahJ in Complex with 5-Methylsalicyl Adenylate -

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Basic information

Entry
Database: PDB / ID: 5wm5
TitleCrystal Structure of CahJ in Complex with 5-Methylsalicyl Adenylate
ComponentsSalicylate-AMP ligase
KeywordsLIGASE / Adenylation Domain / Peptide Synthetase
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds / nucleotide binding / metal ion binding
Similarity search - Function
: / ANL, N-terminal domain / 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 ...: / ANL, N-terminal domain / 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-B5Y / Salicylate-AMP ligase
Similarity search - Component
Biological speciesStreptomyces gandocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.797 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Salicylate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4755
Polymers60,7841
Non-polymers6924
Water9,710539
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)121.711, 121.711, 87.825
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-872-

HOH

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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-B5Y / 9-(5-O-{(S)-hydroxy[(2-hydroxy-5-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine


Mass: 481.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N5O9P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.19 %
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

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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: Jul 6, 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: 0.12
ReflectionResolution: 1.797→45.19 Å / Num. obs: 69222 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.376 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.115 / Χ2: 1.1 / Net I/σ(I): 8.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.797-1.913.3891.21.19111120.4141.42199.2
1.91-2.043.4150.6782.21104650.6820.80299.3
2.04-2.23.2950.3673.8797120.8670.43699.1
2.2-2.413.4840.2345.9989810.9440.27699.2
2.41-2.693.3810.1498.5481410.970.17798.8
2.69-3.113.4380.08713.6172020.9890.10398.9
3.11-3.83.3170.05520.5461250.9940.06699
3.8-5.363.3010.04326.4247560.9960.05198
5.36-45.193.1880.03926.9927280.9970.04797.3

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Processing

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

5wm2


Resolution: 1.797→45.19 Å / Cross valid method: FREE R-VALUE / σ(F): 44.04 / Phase error: 25.5
RfactorNum. reflection% reflection
Rfree0.1971 1147 1.87 %
Rwork0.1538 --
obs0.155 69218 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.59 Å2 / Biso mean: 32.5646 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 1.797→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 47 539 4621
Biso mean--35.86 43.53 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064169
X-RAY DIFFRACTIONf_angle_d0.9255691
X-RAY DIFFRACTIONf_chiral_restr0.054643
X-RAY DIFFRACTIONf_plane_restr0.005758
X-RAY DIFFRACTIONf_dihedral_angle_d10.3662489
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 (%)
1.7987-1.84360.37741310.3297802793381
1.8436-1.89340.30791300.31027958808882
1.8934-1.94910.31871330.27887968810183
1.9491-2.01190.31841190.25267973809283
2.0119-2.08370.24341290.22768108823783
2.0837-2.16710.23091440.20848135827985
2.1671-2.26550.22981360.19928319845586
2.2655-2.38470.17591370.1828322845986
2.3847-2.53380.23171370.17318407854487
2.5338-2.72890.19841450.16758493863888
2.7289-3.00240.18481620.15578625878789
3.0024-3.43450.16841440.13178640878490
3.4345-4.3180.16781440.09868733887790
4.318-18.50720.16371620.10479005916793
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)
13.1989-0.8939-0.62171.7933-0.31043.25070.0830.1817-0.2826-0.25490.04740.10770.4127-0.2451-0.08380.3341-0.0775-0.04670.3049-0.0460.1601-13.56540.8969-13.2634
22.81810.85960.20881.52940.14531.6548-0.02690.012-0.30780.03240.0452-0.08920.29460.0653-0.01610.30320.02170.01080.21630.01110.20191.539633.23067.9838
31.4557-0.3793-0.51181.2569-0.09651.97-0.0611-0.146-0.1578-0.00920.05330.08260.2004-0.24340.00410.2517-0.06750.00530.3060.02360.1725-17.117238.846714.843
41.13020.19420.22250.9785-0.09211.5178-0.06760.0267-0.0478-0.0540.04220.0570.1797-0.13660.03790.2413-0.02190.01680.2433-0.010.1344-8.033843.61330.9368
50.5113-0.07250.02011.24550.33011.1095-0.0224-0.07010.02690.05860.036-0.0985-0.02720.0716-0.01610.1907-0.00510.00530.2412-0.00020.11752.233757.84998.9404
61.51260.72040.08681.48560.0980.7450.01780.09310.078-0.11440.00280.1980.002-0.2176-0.02150.2165-0.0142-0.01890.29920.01550.1111-14.303659.6361-9.5523
71.84360.5038-1.75110.1901-0.44852.06790.01090.0860.17130.02790.09460.0948-0.0529-0.3077-0.04270.22650.0103-0.00940.2924-0.01380.16-18.441964.22912.6379
80.3716-0.23160.02551.3676-0.24610.9911-0.0648-0.04160.06940.19820.07680.104-0.1214-0.2343-0.03350.23450.00620.02850.3351-0.01760.1883-28.57965.945118.3217
92.7603-0.33010.18952.5131-0.33562.97-0.05880.21110.40040.03780.07790.2906-0.4918-0.29070.00910.29440.01160.01450.33860.01020.2687-28.631371.042111.487
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 360 )A256 - 360
6X-RAY DIFFRACTION6chain 'A' and (resid 361 through 433 )A361 - 433
7X-RAY DIFFRACTION7chain 'A' and (resid 434 through 472 )A434 - 472
8X-RAY DIFFRACTION8chain 'A' and (resid 473 through 518 )A473 - 518
9X-RAY DIFFRACTION9chain 'A' and (resid 519 through 553 )A519 - 553

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