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- PDB-5wm4: Crystal Structure of CahJ in Complex with 6-Methylsalicyl Adenylate -

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Basic information

Entry
Database: PDB / ID: 5wm4
TitleCrystal Structure of CahJ in Complex with 6-Methylsalicyl Adenylate
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 / Chem-B5M / Salicylate-AMP ligase
Similarity search - Component
Biological speciesStreptomyces gandocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.781 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)61,82811
Polymers60,7841
Non-polymers1,04410
Water15,655869
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)122.188, 122.188, 88.174
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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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

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Non-polymers , 5 types, 879 molecules

#2: Chemical ChemComp-B5M / 9-(5-O-{(S)-hydroxy[(2-hydroxy-6-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
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: 1.033 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: 1.033 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.83
ReflectionResolution: 1.78→45.368 Å / Num. obs: 72135 / % possible obs: 99.15 % / Observed criterion σ(I): -3 / Redundancy: 3.929 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.104 / Χ2: 0.978 / Net I/σ(I): 10.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.78-1.893.8380.8221.5115720.5170.95499.3
1.89-2.023.9330.5392.45109010.7520.62299.6
2.02-2.183.9810.3114.26101690.880.35999.4
2.18-2.393.8320.2315.7293540.9290.26899.1
2.39-2.674.0490.1399.0885090.9740.1699.7
2.67-3.083.8780.08414.4275130.990.09799.4
3.08-3.774.0590.05124.464050.9960.05899.4
3.77-5.313.9010.03533.8549240.9980.0497.8
5.31-45.3683.9570.03236.627600.9980.03794.8

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Processing

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

5wm2


Resolution: 1.781→40.696 Å / Cross valid method: FREE R-VALUE / σ(F): 58.07 / Phase error: 25.83
RfactorNum. reflection% reflection
Rfree0.1964 1101 1.71 %
Rwork0.1544 --
obs0.2073 72133 99.146 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.17 Å2 / Biso mean: 25.601 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.781→40.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 70 869 4995
Biso mean--29.71 37.66 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074219
X-RAY DIFFRACTIONf_angle_d0.8295753
X-RAY DIFFRACTIONf_chiral_restr0.055647
X-RAY DIFFRACTIONf_plane_restr0.006768
X-RAY DIFFRACTIONf_dihedral_angle_d10.7913446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.781-1.82160.29861430.27588417856095
1.8216-1.8640.25031500.26048298844895
1.864-1.91060.30041290.27278293842294
1.9106-1.96220.26861400.2728293843395
1.9622-2.01990.25141310.22788327845896
2.0199-2.08510.22791280.22338410853896
2.0851-2.15970.23921450.21588393853895
2.1597-2.24610.23121310.22598245837694
2.2461-2.34830.2661430.22418239838294
2.3483-2.47210.22921310.20438433856496
2.4721-2.62690.26141350.20098403853896
2.6269-2.82970.21321510.19968375852695
2.8297-3.11430.25221500.20348283843394
3.1143-3.56460.26231340.20648443857796
3.5646-4.48960.27831310.18548223835494
4.4896-35.75770.20721480.188004815291
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)
12.7427-0.9484-0.87041.2296-0.49482.80490.06820.1108-0.1857-0.1730.01640.06510.1504-0.1235-0.07460.21-0.0313-0.02310.2082-0.04570.1263-13.864341.297-13.3015
24.21191.36820.11781.51270.151.39520.0099-0.0469-0.2410.0738-0.0308-0.08680.10940.04150.02020.16330.0179-0.00440.11260.00720.1190.941633.48858.0878
31.2224-0.3871-0.59231.21010.63711.1874-0.01610.0053-0.0364-0.0380.02040.01340.0066-0.08840.00520.1633-0.01710.00310.16380.02330.1084-15.781340.786710.1549
41.4678-0.50950.43881.28670.07032.395-0.0361-0.0358-0.0802-0.01530.07790.02660.1466-0.0904-0.04540.1751-0.0170.02440.17580.01740.111-19.283337.862620.2629
50.794-0.67090.86681.749-1.44341.3739-0.0033-0.0319-0.1233-0.01770.02790.14080.15020.0054-0.01890.1725-0.05440.0170.1906-0.01580.1528-14.732837.44432.4164
60.35710.08630.07970.62570.12990.3927-0.0032-0.02190.00070.01340.0091-0.0382-0.02090.0011-0.00940.1517-0.00260.00550.1674-0.0020.090.440755.35736.458
70.5055-0.3672-0.24981.1391-0.07510.3130.0026-0.0261-0.0296-0.03380.0134-0.00660.0178-0.0663-0.01340.178-0.01790.0140.18960.01180.0852-2.9263.0174-8.8177
80.60110.0341-0.27140.11970.02920.48540.01610.07030.0565-0.02490.01660.0602-0.0505-0.0622-0.04320.15840.0038-0.01380.1777-0.00440.1331-21.397362.8257-0.012
92.042-0.2683-0.34572.6928-0.3171.5798-0.03470.07980.1931-0.00670.04920.1347-0.1769-0.0213-0.02660.161-0.01640.00110.1741-0.01240.1294-29.907168.494516.0645
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 91 )A47 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 142 )A92 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 189 )A143 - 189
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 218 )A190 - 218
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 360 )A219 - 360
7X-RAY DIFFRACTION7chain 'A' and (resid 361 through 387 )A361 - 387
8X-RAY DIFFRACTION8chain 'A' and (resid 388 through 499 )A388 - 499
9X-RAY DIFFRACTION9chain 'A' and (resid 500 through 554 )A500 - 554

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