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

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Basic information

Entry
Database: PDB / ID: 5ups
TitleAcyl-CoA synthetase PtmA2 from Streptomyces platensis in complex with SBNP663 ligand
ComponentsAcyl-CoA synthetase PtmA2
KeywordsTRANSFERASE / ACYL-COA SYNTHETASE / PTMA2 / STRUCTURAL GENOMICS / APC109894 / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
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 / AMP-binding enzyme, C-terminal domain superfamily ...: / 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 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8K1 / FORMIC ACID / PtmA2
Similarity search - Component
Biological speciesStreptomyces platensis subsp. rosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 ...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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)116,76916
Polymers114,9362
Non-polymers1,83414
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-24 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.669, 162.669, 114.135
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#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
#2: Chemical ChemComp-8K1 / 5'-O-[(R)-hydroxy{[(7beta,8alpha,9beta,10alpha,11beta,13alpha)-7-hydroxy-19-oxo-11,16-epoxykauran-19-yl]oxy}phosphoryl]adenosine


Mass: 663.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42N5O10P
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.2 M sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 108962 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.041 / Rrim(I) all: 0.122 / Χ2: 1.516 / Net I/σ(I): 6.4 / Num. measured all: 939293
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.098.50.8932.050.7490.3240.9510.605100
2.09-2.128.50.7540.8030.2750.8030.635100
2.12-2.168.10.6560.8360.2450.7010.663100
2.16-2.217.70.5620.870.2140.6020.714100
2.21-2.268.90.4920.910.1740.5220.74100
2.26-2.3190.4240.9380.1490.4490.819100
2.31-2.3790.3720.9450.1310.3950.893100
2.37-2.438.90.3120.9570.1110.3310.99100
2.43-2.58.70.2840.9630.1020.3021.049100
2.5-2.588.50.2460.9710.0890.2621.178100
2.58-2.687.70.2090.9740.080.2241.35699.9
2.68-2.7890.1870.9820.0660.1981.415100
2.78-2.919.10.1630.9870.0570.1721.613100
2.91-3.0690.140.990.0490.1481.835100
3.06-3.258.90.1230.9910.0440.1312.032100
3.25-3.5180.1070.9910.040.1142.192100
3.51-3.869.10.0940.9940.0330.12.331100
3.86-4.428.90.0840.9950.030.092.292100
4.42-5.568.30.0820.9950.030.0872.713100
5.56-508.70.0770.9970.0280.0823.957100

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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: 2.05→48.3 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.851 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 5381 4.9 %RANDOM
Rwork0.1558 ---
obs0.1574 103541 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.26 Å2 / Biso mean: 40.071 Å2 / Biso min: 26.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 2.05→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7942 0 124 722 8788
Biso mean--37.24 48.25 -
Num. residues----1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198343
X-RAY DIFFRACTIONr_bond_other_d0.0010.027767
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.96411395
X-RAY DIFFRACTIONr_angle_other_deg0.796317782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85351060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34422.063383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.516151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1071594
X-RAY DIFFRACTIONr_chiral_restr0.0850.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022025
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 397 -
Rwork0.225 7514 -
all-7911 -
obs--99.33 %
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)
10.2147-0.0776-0.04840.1380.01440.0112-0.0264-0.07490.06120.02930.0391-0.04140.00360.0126-0.01270.03660.0346-0.01870.0976-0.02570.023128.266595.521227.0974
20.493-0.01990.05270.1202-0.00750.0059-0.0025-0.0698-0.02110.05470.00510.0058-0.0025-0.0065-0.00260.03060.0111-0.00010.06580.01110.005960.814266.307824.2423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 522
2X-RAY DIFFRACTION1A701 - 706
3X-RAY DIFFRACTION1B601
4X-RAY DIFFRACTION2B3 - 522
5X-RAY DIFFRACTION2B602 - 608

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