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- PDB-5wm3: Crystal Structure of CahJ in Complex with Salicyl Adenylate -

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Basic information

Entry
Database: PDB / ID: 5wm3
TitleCrystal Structure of CahJ in Complex with Salicyl Adenylate
ComponentsSalicylate-AMP ligase
KeywordsLIGASE / Adenylation Domain / Peptide Synthetase.
Function / homology
Function and homology information


ligase activity / nucleotide binding / metal ion binding
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 ...: / 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 / 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-B5V / Salicylate-AMP ligase
Similarity search - Component
Biological speciesStreptomyces gandocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.679 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)61,6368
Polymers60,7841
Non-polymers8537
Water15,583865
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)122.413, 122.413, 88.092
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-1492-

HOH

21A-1529-

HOH

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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, 872 molecules

#2: Chemical ChemComp-B5V / 9-(5-O-{(S)-hydroxy[(2-hydroxybenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine


Mass: 467.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N5O9P
#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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 60.76 %
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: 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: 0.04
ReflectionResolution: 1.679→45.418 Å / Num. obs: 85969 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.386 % / CC1/2: 0.985 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.142 / Χ2: 1.036 / Net I/σ(I): 5.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.679-1.783.3180.5841.54136910.6630.69798.4
1.78-1.93.4050.3842.41130390.8180.45699.6
1.9-2.063.420.2523.72121160.9110.29999.2
2.06-2.253.3470.1765.32111860.9460.2199.1
2.25-2.523.4860.1466.82101430.9580.17499.3
2.52-2.93.3560.1188.4589250.970.14198.6
2.9-3.553.5020.10211.0875610.9780.12198.7
3.55-5.013.3050.09312.6759130.9770.11198
5.01-45.4183.2530.09212.8133950.980.1198

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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: 1.679→45.418 Å / Cross valid method: FREE R-VALUE / σ(F): 52.48 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.2046 1419 1.72 %
Rwork0.1735 --
obs0.1742 85969 98.882 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.03 Å2 / Biso mean: 27.5279 Å2 / Biso min: 12.3 Å2
Refinement stepCycle: final / Resolution: 1.679→45.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 57 865 4981
Biso mean--28.31 41.18 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064208
X-RAY DIFFRACTIONf_angle_d0.8885743
X-RAY DIFFRACTIONf_chiral_restr0.052648
X-RAY DIFFRACTIONf_plane_restr0.005766
X-RAY DIFFRACTIONf_dihedral_angle_d11.0293429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6795-1.71010.3111300.33928108823892
1.7101-1.7430.30641310.31218154828592
1.743-1.77850.26721390.29518256839593
1.7785-1.81720.3011340.27368168830293
1.8172-1.85950.26181500.25318390854095
1.8595-1.9060.2511400.24178434857495
1.906-1.95750.23691430.22358421856495
1.9575-2.01510.25481360.21798329846594
2.0151-2.08010.2041280.21088170829892
2.0801-2.15450.21091470.20148400854794
2.1545-2.24070.21411370.19518367850495
2.2407-2.34270.21431420.19158514865696
2.3427-2.46620.19271390.18758504864396
2.4662-2.62060.21991370.18488214835193
2.6206-2.82290.19051430.16918369851294
2.8229-3.10690.21311500.16138479862996
3.1069-3.55610.17381370.13998385852295
3.5561-4.47890.17471310.11368166829792
4.4789-35.75920.17961510.1328358850994
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)
14.043-1.4809-0.64631.5638-0.07933.47880.0210.1177-0.3532-0.19460.01790.13830.1689-0.1838-0.02020.2478-0.0429-0.030.229-0.05040.1803-13.763641.3972-13.2627
23.72381.11990.36531.77150.33831.6076-0.0405-0.0142-0.31210.09970.016-0.08360.13070.03390.0170.20840.02270.00050.15530.00220.18890.983933.57188.1251
31.3414-0.4346-0.73931.0732-0.03571.8851-0.0392-0.0199-0.07930.02430.00840.01320.1068-0.1280.02590.1758-0.03850.0030.19770.00360.1589-17.358639.383714.9659
41.09110.03480.00560.92740.05641.4344-0.01460.0094-0.0501-0.0299-0.00080.05180.1083-0.09120.02350.171-0.01150.00820.1704-0.01460.1321-8.353344.20150.982
50.50210.03930.10811.11070.18230.8-0.0145-0.01580.0090.05770.0342-0.0743-0.01410.0235-0.01880.1536-0.00160.00540.1902-0.0050.12732.070358.29918.9186
62.49931.20960.2391.5610.22410.4548-0.00080.08240.0991-0.1242-0.00950.1748-0.0215-0.11020.01350.19150.0001-0.0190.22790.0070.1081-14.343259.9667-9.4231
71.3640.1631-1.27950.3168-0.0831.3310.030.06030.11310.02290.0290.0898-0.024-0.1333-0.04690.12710.0031-0.00490.1898-0.01060.1417-21.513266.30287.3825
82.17010.236-0.80012.8884-0.24841.9812-0.05510.11780.3481-0.11120.13060.2793-0.1925-0.18-0.08320.1542-0.0121-0.02850.22890.00010.2025-30.254468.600115.5609
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 189 )A92 - 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 499 )A434 - 499
8X-RAY DIFFRACTION8chain 'A' and (resid 500 through 554 )A500 - 554

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