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- PDB-5upq: Acyl-CoA synthetase PtmA2 from Streptomyces platensis in complex ... -

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Basic information

Entry
Database: PDB / ID: 5upq
TitleAcyl-CoA synthetase PtmA2 from Streptomyces platensis in complex with SBNP465 ligand
ComponentsAcyl-CoA synthetase PtmA2
KeywordsTRANSFERASE / acyl-CoA synthetase / PtmA2 / structural genomics / APC109894 / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / PSI-Biology
Function / homology
Function and homology information


ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold ...ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / 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
Biological speciesStreptomyces platensis subsp. rosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsOsipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Rudolf, J.D. / Chang, C.Y. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. ...Osipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Rudolf, J.D. / Chang, C.Y. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme.
Authors: Wang, N. / Rudolf, J.D. / Dong, L.B. / Osipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Chang, C.Y. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionFeb 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references / Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA synthetase PtmA2
B: Acyl-CoA synthetase PtmA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,71421
Polymers114,9362
Non-polymers2,77919
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-152 kcal/mol
Surface area40400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.608, 145.737, 145.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acyl-CoA synthetase PtmA2


Mass: 57467.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis subsp. rosaceus (bacteria)
Plasmid: PMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A0V031

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Non-polymers , 5 types, 231 molecules

#2: Chemical ChemComp-8JJ / 5'-O-[(R)-{[(7beta,8alpha,9beta,10alpha,13alpha,16beta)-7,16-dihydroxy-18-oxokauran-18-yl]oxy}(hydroxy)phosphoryl]adenosine


Mass: 665.672 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H44N5O10P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis Tris Propane buffer, 1.5 M lithium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.42→38.5 Å / Num. obs: 57650 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.05 / Rrim(I) all: 0.133 / Χ2: 1.309 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.42-2.4670.9092.20.6170.3680.9820.86399.5
2.46-2.5170.8050.650.3240.8690.87699.5
2.51-2.5570.7340.7190.2960.7930.90299.7
2.55-2.6170.5910.7860.2370.6370.89499.1
2.61-2.6670.5150.8120.2080.5570.92799.7
2.66-2.737.10.4880.8560.1970.5260.93699.6
2.73-2.7970.4050.8880.1640.4380.9999.8
2.79-2.877.10.3310.9130.1330.3581.03599.7
2.87-2.957.10.2790.9410.1130.3021.07899.8
2.95-3.0570.2250.960.0910.2431.15999.7
3.05-3.1670.1860.9690.0750.21.21699.8
3.16-3.287.10.1520.9790.0610.1641.35799.9
3.28-3.437.10.1270.9860.0510.1371.48299.7
3.43-3.617.20.1050.9880.0420.1131.538100
3.61-3.847.20.0950.990.0380.1021.651100
3.84-4.147.30.0890.9910.0350.0961.65199.9
4.14-4.557.20.0870.9910.0350.0941.62299.9
4.55-5.217.10.0850.990.0340.0921.609100
5.21-6.566.90.0820.9930.0330.0891.862100
6.56-506.70.070.9970.0280.0752.38299.2

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7Q

5e7q


Resolution: 2.42→38.5 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.863 / SU B: 20.665 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.268
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 2820 4.9 %RANDOM
Rwork0.2315 ---
obs0.2341 54772 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.69 Å2 / Biso mean: 46.854 Å2 / Biso min: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å2-0 Å2
2---0.64 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.42→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7662 0 166 212 8040
Biso mean--50.57 41.8 -
Num. residues----1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198016
X-RAY DIFFRACTIONr_bond_other_d0.0030.027424
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.97110945
X-RAY DIFFRACTIONr_angle_other_deg0.786316983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39522.207367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.629151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1141587
X-RAY DIFFRACTIONr_chiral_restr0.0720.21199
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021916
LS refinement shellResolution: 2.412→2.474 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 175 -
Rwork0.286 3815 -
all-3990 -
obs--94.93 %
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)
10.781-0.17510.22640.0602-0.02820.09720.00530.03280.00210.0094-0.00170.00160.0097-0.0094-0.00370.00810.0151-0.00810.08780.00450.081423.312184.986221.3474
20.0209-0.02890.02730.2238-0.24370.36850.0155-0.0463-0.0391-0.02070.08070.01310.0613-0.0163-0.09620.0219-0.0012-0.05690.13560.03030.172827.566757.716449.4498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 513
2X-RAY DIFFRACTION1A701 - 709
3X-RAY DIFFRACTION2B2 - 513
4X-RAY DIFFRACTION2B701 - 710

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