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- PDB-5e7q: Acyl-CoA synthetase PtmA2 from Streptomyces platensis -

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Basic information

Entry
Database: PDB / ID: 5e7q
TitleAcyl-CoA synthetase PtmA2 from Streptomyces platensis
Componentsacyl-CoA synthetase
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


catalytic activity / ATP binding
Similarity search - Function
: / 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 ...: / 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 / SAD / Resolution: 2.23 Å
AuthorsOsipiuk, J. / Cuff, M.E. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Rudolf, J. / Ma, M. / Chang, C.Y. / Shen, B. / Phillips Jr., G.N. ...Osipiuk, J. / Cuff, M.E. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Rudolf, J. / Ma, M. / Chang, C.Y. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
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
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references / Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
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 / _citation_author.name
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acyl-CoA synthetase
B: acyl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,71923
Polymers114,7092
Non-polymers2,00921
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-217 kcal/mol
Surface area40560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.872, 146.892, 146.928
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein acyl-CoA synthetase / PtmA2


Mass: 57354.645 Da / Num. of mol.: 2 / Mutation: A141P, G246D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis subsp. rosaceus (bacteria)
Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A0V031
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M magnesium sulfate, 0.1 M MES buffer

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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: Aug 19, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. all: 75465 / Num. obs: 75465 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Rrim(I) all: 0.103 / Χ2: 1.544 / Net I/av σ(I): 22.956 / Net I/σ(I): 9.4 / Num. measured all: 462242
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.23-2.274.10.7011.9537530.6970.3890.8060.92599.9
2.27-2.314.80.62137050.7860.3160.6990.93100
2.31-2.355.50.5937310.7930.2790.6540.976100
2.35-2.45.90.49837100.870.2270.5480.964100
2.4-2.456.40.42837180.9110.1840.4670.977100
2.45-2.516.50.37937370.9250.1630.4131.016100
2.51-2.576.50.33436970.940.1430.3641.052100
2.57-2.646.50.26637850.9630.1140.291.096100
2.64-2.726.50.24737420.9670.1060.2691.146100
2.72-2.816.50.20437480.9760.0870.2221.233100
2.81-2.916.50.16337210.9850.070.1781.323100
2.91-3.036.50.13437380.9890.0570.1461.455100
3.03-3.166.50.11537610.9910.0490.1251.563100
3.16-3.336.40.09337860.9940.0390.1011.686100
3.33-3.546.40.07638050.9960.0320.0831.753100
3.54-3.816.40.06837530.9970.0290.0741.833100
3.81-4.26.40.06438220.9970.0270.071.978100
4.2-4.86.30.06938150.9960.0290.0762.133100
4.8-6.056.20.07138750.9960.030.0772.597100
6.05-505.90.05440630.9980.0240.0593.69699.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.23→48.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.563 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3713 4.9 %RANDOM
Rwork0.1732 ---
obs0.1748 71661 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.96 Å2 / Biso mean: 43.56 Å2 / Biso min: 27.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20 Å2
2--0.38 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.23→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7812 0 107 357 8276
Biso mean--75.36 44.29 -
Num. residues----1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198187
X-RAY DIFFRACTIONr_bond_other_d0.0010.027589
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.95711173
X-RAY DIFFRACTIONr_angle_other_deg0.771317365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88151040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69922.176386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.299151169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9441594
X-RAY DIFFRACTIONr_chiral_restr0.0780.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021979
X-RAY DIFFRACTIONr_mcbond_it1.9813.1834094
X-RAY DIFFRACTIONr_mcbond_other1.983.1834093
X-RAY DIFFRACTIONr_mcangle_it3.024.7625117
LS refinement shellResolution: 2.231→2.289 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 281 -
Rwork0.252 5177 -
all-5458 -
obs--98.63 %
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)
10.7654-0.1621-0.23750.448-0.22040.37720.0515-0.0939-0.0889-0.0136-0.0138-0.04140.03110.0343-0.03760.02490.0017-0.05180.05920.00150.119128.916658.370749.9934
20.82920.18530.18630.3358-0.21390.43670.05840.09450.0944-0.0268-0.03830.02590.0209-0.0395-0.02010.02020.0422-0.00590.10890.00220.072124.231986.691421.6435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 711
2X-RAY DIFFRACTION2B1 - 711

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