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

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Basic information

Entry
Database: PDB / ID: 5upt
TitleAcyl-CoA synthetase PtmA2 from Streptomyces platensis in complex with SBNP468 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


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 / MOLECULAR REPLACEMENT / Resolution: 1.92 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,98510
Polymers57,4681
Non-polymers1,5179
Water6,810378
1
A: Acyl-CoA synthetase PtmA2
hetero molecules

A: Acyl-CoA synthetase PtmA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,97020
Polymers114,9362
Non-polymers3,03418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6340 Å2
ΔGint-98 kcal/mol
Surface area39320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.158, 146.158, 71.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acyl-CoA synthetase PtmA2


Mass: 57467.809 Da / Num. of mol.: 1
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, 387 molecules

#2: Chemical ChemComp-8JG / (7alpha,8alpha,10alpha,13alpha)-7,16-dihydroxykauran-18-oic acid


Mass: 336.466 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H32O4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis_Tris Propane buffer, 1.5 M lithium sulfate, 0.01 M Hexammine cobalt chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 59353 / % possible obs: 99.5 % / Redundancy: 9 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Χ2: 1.862 / Net I/σ(I): 11.5 / Num. measured all: 532202
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-1.955.90.8412.20.660.3770.9261.24798.7
1.95-1.996.40.7470.7010.3250.8181.29399
1.99-2.036.80.6160.7920.2570.671.29399
2.03-2.077.20.520.8480.210.5631.36899.3
2.07-2.117.60.4270.9040.1680.461.41198.9
2.11-2.1680.3830.9190.1460.4111.42899.2
2.16-2.228.60.3440.9390.1260.3671.47599.4
2.22-2.289.50.2990.9570.1040.3171.57299.8
2.28-2.349.60.2650.9710.0910.2811.64599.7
2.34-2.429.70.2250.9780.0770.2381.6999.9
2.42-2.519.80.1970.9840.0670.2091.769100
2.51-2.619.90.1680.9890.0570.1781.79999.9
2.61-2.72100.1470.990.0490.1551.866100
2.72-2.8710.10.1250.9950.0410.1321.939100
2.87-3.0510.20.1020.9950.0340.1072.026100
3.05-3.2810.20.0850.9960.0280.0892.154100
3.28-3.6110.10.0670.9980.0220.072.197100
3.61-4.1410.10.0580.9980.0190.0612.31100
4.14-5.219.90.0560.9980.0180.0592.42999.9
5.21-509.10.0740.9960.0260.0793.09898.5

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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: 1.92→36.2 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.328 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 2994 5.1 %RANDOM
Rwork0.1642 ---
obs0.1658 56197 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.13 Å2 / Biso mean: 31.291 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.92→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 100 378 4423
Biso mean--49.28 42.05 -
Num. residues----515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194185
X-RAY DIFFRACTIONr_bond_other_d0.0010.023916
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9785739
X-RAY DIFFRACTIONr_angle_other_deg0.82938977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49422.304191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44815583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6921545
X-RAY DIFFRACTIONr_chiral_restr0.0980.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02991
LS refinement shellResolution: 1.916→1.965 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 186 -
Rwork0.252 4023 -
all-4209 -
obs--97.77 %
Refinement TLS params.Method: refined / Origin x: 21.558 Å / Origin y: 49.684 Å / Origin z: 37.9704 Å
111213212223313233
T0.0355 Å20.006 Å20.0063 Å2-0.0426 Å2-0.0158 Å2--0.0095 Å2
L0.0794 °2-0.0721 °2-0.0135 °2-0.078 °20.0514 °2--0.3419 °2
S-0.0052 Å °0.0058 Å °-0.0033 Å °-0.0134 Å °-0.0225 Å °0.006 Å °-0.0378 Å °-0.0453 Å °0.0278 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 513
2X-RAY DIFFRACTION1A701 - 709

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