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- PDB-5es8: Crystal structure of the initiation module of LgrA in the thiolat... -

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Basic information

Entry
Database: PDB / ID: 5es8
TitleCrystal structure of the initiation module of LgrA in the thiolation state
ComponentsLinear gramicidin synthetase subunit A
KeywordsLIGASE / NRPS / formylation domain / adenylation domain / peptidyl carrier protein
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / antibiotic biosynthetic process / cytosol
Similarity search - Function
Non-ribosomal peptide synthase / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site ...Non-ribosomal peptide synthase / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Chem-5S4 / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.547 Å
AuthorsReimer, J.M. / Aloise, M.N. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106615 Canada
CitationJournal: Nature / Year: 2016
Title: Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase.
Authors: Reimer, J.M. / Aloise, M.N. / Harrison, P.M. / Schmeing, T.M.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Linear gramicidin synthetase subunit A
B: Linear gramicidin synthetase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,0074
Polymers176,1262
Non-polymers8812
Water34219
1
A: Linear gramicidin synthetase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5042
Polymers88,0631
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Linear gramicidin synthetase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5042
Polymers88,0631
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.550, 101.050, 138.740
Angle α, β, γ (deg.)90.000, 91.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 1 - 770 / Label seq-ID: 1 - 770

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Linear gramicidin synthetase subunit A


Mass: 88063.180 Da / Num. of mol.: 2 / Fragment: UNP residues 2-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: lgrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70LM7
#2: Chemical ChemComp-5S4 / [(3~{R})-4-[[3-[2-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate


Type: peptide-like / Mass: 440.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H33N4O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 20 000, 0.1 M MES pH 6.7

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.547→47.472 Å / Num. obs: 65693 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.075 / Rrim(I) all: 0.12 / Χ2: 0.901 / Net I/av σ(I): 11.245 / Net I/σ(I): 6.8 / Num. measured all: 224938
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.6-2.642.932030.5350.8780.6898.2
2.64-2.693.232760.4870.8260.69199.3
2.69-2.743.332620.5960.7520.67899.7
2.74-2.83.433110.6550.6980.7499.8
2.8-2.863.532830.7160.5810.76199.70.923
2.86-2.933.632690.8180.4570.80799.60.7290.862
2.93-33.633330.7710.4130.81699.60.6560.777
3-3.083.632670.8330.3430.89699.40.5450.646
3.08-3.173.632940.8860.270.93499.30.430.509
3.17-3.283.632710.9270.2091.004990.3310.393
3.28-3.393.632870.9460.170.97598.60.270.32
3.39-3.533.532480.9680.1270.9798.80.1980.236
3.53-3.693.532680.9790.10.98298.60.1580.187
3.69-3.883.532840.9870.0751.01798.70.1170.139
3.88-4.133.532810.9890.061.07990.0930.111
4.13-4.453.532690.9890.0510.97498.80.080.095
4.45-4.893.433180.9880.050.98398.80.0760.091
4.89-5.63.433010.9890.0490.98398.60.0740.089
5.6-7.053.433010.990.0460.96898.70.0710.085
7.05-50333670.9940.0381.0198.20.0530.066

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ES6

5es6


Resolution: 2.547→47.472 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 3264 5.01 %
Rwork0.2247 61825 -
obs0.2272 65089 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.06 Å2 / Biso mean: 83.3022 Å2 / Biso min: 40.51 Å2
Refinement stepCycle: final / Resolution: 2.547→47.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12180 0 56 19 12255
Biso mean--82.85 64.75 -
Num. residues----1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712517
X-RAY DIFFRACTIONf_angle_d1.14617000
X-RAY DIFFRACTIONf_chiral_restr0.051869
X-RAY DIFFRACTIONf_plane_restr0.0062214
X-RAY DIFFRACTIONf_dihedral_angle_d14.2944650
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7075X-RAY DIFFRACTION10.505TORSIONAL
12B7075X-RAY DIFFRACTION10.505TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5469-2.58490.951190.88811041134
2.5849-2.62530.4241170.40682247236480
2.6253-2.66830.37461470.36822834298199
2.6683-2.71430.41291440.33142802294699
2.7143-2.76370.37521490.323828402989100
2.7637-2.81680.34251570.30492848300599
2.8168-2.87430.34311470.2952826297399
2.8743-2.93680.36051520.29582789294199
2.9368-3.00510.34821470.29722868301599
3.0051-3.08020.39251520.29932814296699
3.0802-3.16350.39971470.28432850299799
3.1635-3.25660.34181480.27342814296299
3.2566-3.36160.32851450.26792824296999
3.3616-3.48180.3281520.25262828298099
3.4818-3.62110.29421460.25152799294599
3.6211-3.78590.30471500.23692813296399
3.7859-3.98540.25571490.20712847299699
3.9854-4.23490.22241520.19652841299399
4.2349-4.56170.23491570.1822808296599
4.5617-5.02030.22721470.17962841298899
5.0203-5.74560.23261470.19712834298198
5.7456-7.23480.25081500.20572860301099
7.2348-47.48050.20211530.17492894304798

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