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- PDB-5wm7: Crystal Structure of CahJ in Complex with AMP -

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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 / 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 / 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

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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)61,2824
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

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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-AMP / 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


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


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


Mass: 18.015 Da / Num. of mol.: 385 / 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: 3.11 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

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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 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

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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

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