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- PDB-6tm4: NatL2 in complex with two molecules of salicylic acid -

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Basic information

Entry
Database: PDB / ID: 6tm4
TitleNatL2 in complex with two molecules of salicylic acid
Components(PaaK-like ligase (AMP-dependent synthetase and ...) x 2
KeywordsLIGASE / phenyl acetate CoA ligase
Function / homologyANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / ligase activity / nucleotide binding / metal ion binding / ADENOSINE MONOPHOSPHATE / 2-HYDROXYBENZOIC ACID / AMP-dependent synthetase and ligase
Function and homology information
Biological speciesStreptomyces sp. Tu 6176 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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
DepositionDec 3, 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 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: PaaK-like ligase (AMP-dependent synthetase and ligase)
BBB: PaaK-like ligase (AMP-dependent synthetase and ligase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,73011
Polymers96,6502
Non-polymers1,0799
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-40 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.460, 139.240, 129.660
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
11BBB-661-

HOH

21BBB-692-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

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

#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(DE3) (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(DE3) (bacteria) / References: UniProt: A0A022MRT4

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Non-polymers , 5 types, 169 molecules

#3: Chemical
ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M KSCN, 0.1 M sodium citrate pH 6, 24-32% PEG MME 2K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.89→71.13 Å / Num. obs: 77807 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.4
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5703 / CC1/2: 0.65 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SIW

6siw


Resolution: 1.89→71.128 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.202 / SU B: 10.773 / SU ML: 0.143 / Average fsc free: 0.8366 / Average fsc work: 0.8455 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2303 3811 4.9 %
Rwork0.1978 73962 -
all0.199 --
obs-77773 99.949 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.313 Å2
Baniso -1Baniso -2Baniso -3
1--2.732 Å20 Å20 Å2
2--3.626 Å20 Å2
3----0.894 Å2
Refinement stepCycle: LAST / Resolution: 1.89→71.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 67 160 6954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136958
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176440
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6669490
X-RAY DIFFRACTIONr_angle_other_deg1.3061.57314836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43719.742388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.626151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4461577
X-RAY DIFFRACTIONr_chiral_restr0.0670.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021585
X-RAY DIFFRACTIONr_nbd_refined0.1930.21270
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.26053
X-RAY DIFFRACTIONr_nbtor_refined0.1610.23316
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23174
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2260
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.217
X-RAY DIFFRACTIONr_nbd_other0.2180.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.28
X-RAY DIFFRACTIONr_mcbond_it1.7952.8313444
X-RAY DIFFRACTIONr_mcbond_other1.7922.833443
X-RAY DIFFRACTIONr_mcangle_it2.7344.2364298
X-RAY DIFFRACTIONr_mcangle_other2.7344.2374299
X-RAY DIFFRACTIONr_scbond_it2.1963.083514
X-RAY DIFFRACTIONr_scbond_other2.1953.083513
X-RAY DIFFRACTIONr_scangle_it3.4784.5185192
X-RAY DIFFRACTIONr_scangle_other3.4784.5185193
X-RAY DIFFRACTIONr_lrange_it5.32232.4627546
X-RAY DIFFRACTIONr_lrange_other5.32332.4067529
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0512963
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.89-1.9390.3752720.34854260.3556990.4150.44999.98250.328
1.939-1.9920.3142910.32852520.32755450.5530.51799.96390.305
1.992-2.050.2982840.29151240.29154090.7650.75399.98150.263
2.05-2.1130.2832380.26450190.26552570.8310.8271000.235
2.113-2.1820.2972820.24747900.2550750.8430.85799.94090.22
2.182-2.2590.2682270.22647230.22749510.8650.88999.97980.2
2.259-2.3440.252230.2145230.21247470.9060.91799.97890.187
2.344-2.4390.2532460.20743650.20946120.9170.92199.97830.186
2.439-2.5480.2611990.20141680.20343700.9180.93499.93140.18
2.548-2.6720.2242380.20240000.20342410.930.93599.92930.184
2.672-2.8160.2452030.19837880.239910.9190.9381000.186
2.816-2.9870.2471850.20536300.20738170.9220.93499.94760.201
2.987-3.1930.2511560.21334340.21535910.9210.93399.97220.211
3.193-3.4480.2141400.231830.20133270.9450.95299.87980.206
3.448-3.7760.2271590.18629360.18830950.9410.9551000.198
3.776-4.220.21420.16526670.16728130.9590.96599.85780.19
4.22-4.870.178990.14823970.14924970.9690.97499.960.178
4.87-5.9580.206960.16820150.16921140.9580.96699.85810.203
5.958-8.3960.169860.15715850.15716750.970.97199.76120.196
8.396-71.1280.183450.1769370.1779860.9750.9799.59430.229
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)
11.1214-0.20070.42870.8580.41772.34420.0694-0.3842-0.43820.11730.0919-0.00880.5452-0.177-0.16130.1326-0.0412-0.03670.15670.1670.2021-31.2548-24.1558-13.5355
22.1166-0.59060.03120.74720.1171.3540.02710.11350.0442-0.2015-0.0113-0.0723-0.10310.1079-0.01580.1206-0.0313-0.01740.02730.01070.0391-26.1609-8.9329-42.3715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA*4 - 601
2X-RAY DIFFRACTION2ALLB*0 - 801

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