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- PDB-6siw: PaaK family AMP-ligase with AMP -

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Basic information

Entry
Database: PDB / ID: 6siw
TitlePaaK family AMP-ligase with AMP
Components(PaaK-like ligase (AMP-dependent synthetase and ...) x 2
KeywordsLIGASE / PaaK like ligase
Function / homology
Function and homology information


ligase activity / nucleotide binding / metal ion binding
Similarity search - Function
ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme
Similarity search - Domain/homology
Chem-7PE / ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / AMP-dependent synthetase and ligase
Similarity search - Component
Biological speciesStreptomyces sp. Tu 6176 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å
AuthorsNaismith, J.H. / Song, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: The Biosynthesis of the Benzoxazole in Nataxazole Proceeds via an Unstable Ester and has Synthetic Utility.
Authors: Song, H. / Rao, C. / Deng, Z. / Yu, Y. / Naismith, J.H.
History
DepositionAug 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PaaK-like ligase (AMP-dependent synthetase and ligase)
B: PaaK-like ligase (AMP-dependent synthetase and ligase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,55619
Polymers96,6502
Non-polymers1,90617
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13690 Å2
ΔGint-45 kcal/mol
Surface area31630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.131, 138.094, 130.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

21A-705-

HOH

31B-715-

HOH

41B-723-

HOH

51B-730-

HOH

61B-732-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 5 - 435

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA5 - 435
2BB6 - 436

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Components

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PaaK-like ligase (AMP-dependent synthetase and ... , 2 types, 2 molecules AB

#1: Protein PaaK-like ligase (AMP-dependent synthetase and ligase) / Coenzyme F390 synthetase


Mass: 48289.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natL2, CF54_07380 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A022MRT4
#2: Protein PaaK-like ligase (AMP-dependent synthetase and ligase) / Coenzyme F390 synthetase


Mass: 48360.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natL2, CF54_07380 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A022MRT4

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Non-polymers , 7 types, 278 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M KSCN, 0.1 M sodium citrate pH 6.0, 30% PEG MME 2K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0056 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0056 Å / Relative weight: 1
ReflectionResolution: 1.96→84.65 Å / Num. obs: 69487 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.8
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 10 % / Rmerge(I) obs: 0.901 / Num. unique obs: 3406 / CC1/2: 0.522 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.96→84.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.147 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.158
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 3574 5.2 %RANDOM
Rwork0.1995 ---
obs0.2014 65021 98.68 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 159.3 Å2 / Biso mean: 41.282 Å2 / Biso min: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å20 Å20 Å2
2--3.14 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.96→84.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6752 0 117 261 7130
Biso mean--49.38 40.51 -
Num. residues----865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176597
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.669662
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5715211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1319.722396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3911579
X-RAY DIFFRACTIONr_chiral_restr0.0660.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021598
Refine LS restraints NCS

Ens-ID: 1 / Number: 13236 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 269 -
Rwork0.414 4562 -
all-4831 -
obs--95.32 %
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)
10.59360.02020.13230.9355-0.09781.21530.0148-0.195-0.21220.06690.04130.05840.2066-0.0857-0.0560.0438-0.0107-0.00850.0750.09410.1409-31.2812-23.9842-13.5701
20.8782-0.08650.19341.104-0.19111.1768-0.13640.1264-0.0071-0.29710.09390.0405-0.07690.04460.04250.1382-0.0679-0.04780.04060.02840.0566-26.1519-9.0029-42.55
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 607
2X-RAY DIFFRACTION2B0 - 701

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