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- PDB-5jnf: Crystal structure of the LgrA initiation module excluding the Asu... -

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Basic information

Entry
Database: PDB / ID: 5jnf
TitleCrystal structure of the LgrA initiation module excluding the Asub domain: F-A-delta-sub
ComponentsLinear gramicidin synthase subunit A
KeywordsLIGASE / NRPS / formylation domain / adenylation domain
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / ligase activity / phosphopantetheine binding / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Non-ribosomal peptide synthase / Formyl transferase, N-terminal domain / 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 ...Non-ribosomal peptide synthase / Formyl transferase, N-terminal domain / 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 / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsReimer, J.M. / Aloise, M.N. / Schmeing, T.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Manipulation of an existing crystal form unexpectedly results in interwoven packing networks with pseudo-translational symmetry
Authors: Reimer, J.M. / Aloise, M.N. / Powell, H.R. / Schmeing, T.M.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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
C: Linear gramicidin synthase subunit A
A: Linear gramicidin synthase subunit A
B: Linear gramicidin synthase subunit A
D: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,3439
Polymers265,1134
Non-polymers2305
Water3,243180
1
C: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4625
Polymers66,2781
Non-polymers1844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3242
Polymers66,2781
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Linear gramicidin synthase subunit A


Theoretical massNumber of molelcules
Total (without water)66,2781
Polymers66,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Linear gramicidin synthase subunit A


Theoretical massNumber of molelcules
Total (without water)66,2781
Polymers66,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.311, 161.311, 139.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2 or (resid 3 and (name...
21(chain B and (resseq 2 or (resid 3 and (name...
31(chain C and (resseq 2 or (resid 3 and (name...
41(chain D and (resseq 2:12 or resseq 14:15 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY(chain A and (resseq 2 or (resid 3 and (name...AB24
12ARGARGARGARG(chain A and (resseq 2 or (resid 3 and (name...AB35
13METMETASPASP(chain A and (resseq 2 or (resid 3 and (name...AB1 - 5853 - 587
14METMETASPASP(chain A and (resseq 2 or (resid 3 and (name...AB1 - 5853 - 587
15METMETASPASP(chain A and (resseq 2 or (resid 3 and (name...AB1 - 5853 - 587
16METMETASPASP(chain A and (resseq 2 or (resid 3 and (name...AB1 - 5853 - 587
17METMETASPASP(chain A and (resseq 2 or (resid 3 and (name...AB1 - 5853 - 587
18METMETASPASP(chain A and (resseq 2 or (resid 3 and (name...AB1 - 5853 - 587
21GLYGLYGLYGLY(chain B and (resseq 2 or (resid 3 and (name...BC24
22ARGARGARGARG(chain B and (resseq 2 or (resid 3 and (name...BC35
23METMETASPASP(chain B and (resseq 2 or (resid 3 and (name...BC1 - 5853 - 587
24METMETASPASP(chain B and (resseq 2 or (resid 3 and (name...BC1 - 5853 - 587
25METMETASPASP(chain B and (resseq 2 or (resid 3 and (name...BC1 - 5853 - 587
26METMETASPASP(chain B and (resseq 2 or (resid 3 and (name...BC1 - 5853 - 587
27METMETASPASP(chain B and (resseq 2 or (resid 3 and (name...BC1 - 5853 - 587
28METMETASPASP(chain B and (resseq 2 or (resid 3 and (name...BC1 - 5853 - 587
31GLYGLYGLYGLY(chain C and (resseq 2 or (resid 3 and (name...CA24
32ARGARGARGARG(chain C and (resseq 2 or (resid 3 and (name...CA35
33METMETASPASP(chain C and (resseq 2 or (resid 3 and (name...CA1 - 5853 - 587
34METMETASPASP(chain C and (resseq 2 or (resid 3 and (name...CA1 - 5853 - 587
35METMETASPASP(chain C and (resseq 2 or (resid 3 and (name...CA1 - 5853 - 587
36METMETASPASP(chain C and (resseq 2 or (resid 3 and (name...CA1 - 5853 - 587
37METMETASPASP(chain C and (resseq 2 or (resid 3 and (name...CA1 - 5853 - 587
38METMETASPASP(chain C and (resseq 2 or (resid 3 and (name...CA1 - 5853 - 587
41GLYGLYSERSER(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD2 - 124 - 14
42GLYGLYASNASN(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD14 - 1516 - 17
43LYSLYSLYSLYS(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD1618
44METMETASPASP(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD1 - 5853 - 587
45METMETASPASP(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD1 - 5853 - 587
46METMETASPASP(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD1 - 5853 - 587
47METMETASPASP(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD1 - 5853 - 587
48METMETASPASP(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD1 - 5853 - 587
49METMETASPASP(chain D and (resseq 2:12 or resseq 14:15 or (resid...DD1 - 5853 - 587

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Components

#1: Protein
Linear gramicidin synthase subunit A


Mass: 66278.227 Da / Num. of mol.: 4 / Fragment: UNP residues 2-584
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-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.3 M sodium formate, 0.1 M triNa citrate pH 5.6.

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Data collection

DiffractionMean temperature: 199 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→88.4 Å / Num. obs: 116252 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 64.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.059 / Rrim(I) all: 0.159 / Net I/σ(I): 8 / Num. measured all: 867930 / Scaling rejects: 10485
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.55-2.66.32.2453636757600.1690.9762.4530.8100
13.98-88.47.20.05152437310.9990.020.05522.397.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ES6

5es6


Resolution: 2.75→44.793 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 9162 5.01 %
Rwork0.2472 173730 -
obs0.2486 116116 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.24 Å2 / Biso mean: 106.3871 Å2 / Biso min: 31.33 Å2
Refinement stepCycle: final / Resolution: 2.75→44.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18470 0 25 180 18675
Biso mean--74.41 62.29 -
Num. residues----2329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418901
X-RAY DIFFRACTIONf_angle_d0.64225661
X-RAY DIFFRACTIONf_chiral_restr0.0492838
X-RAY DIFFRACTIONf_plane_restr0.0043354
X-RAY DIFFRACTIONf_dihedral_angle_d19.1616942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12773X-RAY DIFFRACTION9.755TORSIONAL
12B12773X-RAY DIFFRACTION9.755TORSIONAL
13C12773X-RAY DIFFRACTION9.755TORSIONAL
14D12773X-RAY DIFFRACTION9.755TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.78130.42023070.427858576164100
2.7813-2.8140.40073110.411457016012100
2.814-2.84830.36893180.398758276145100
2.8483-2.88430.4072820.366458636145100
2.8843-2.92230.38183080.358857406048100
2.9223-2.96230.38363060.339357536059100
2.9623-3.00460.33973300.327358646194100
3.0046-3.04950.3123080.309257636071100
3.0495-3.09710.33873160.294557806096100
3.0971-3.14790.37623130.31458686181100
3.1479-3.20210.36743050.300556525957100
3.2021-3.26030.36013160.303758616177100
3.2603-3.3230.32313080.273457536061100
3.323-3.39080.29553060.266258056111100
3.3908-3.46450.3552920.35245759605199
3.4645-3.54510.27033000.269658076107100
3.5451-3.63370.34213080.265557546062100
3.6337-3.73190.31053030.312758636166100
3.7319-3.84170.28123060.247757936099100
3.8417-3.96560.29062940.29475662595699
3.9656-4.10720.24492940.20658806174100
4.1072-4.27160.21753020.195658066108100
4.2716-4.46580.21793190.200357906109100
4.4658-4.7010.21732870.191357626049100
4.701-4.99520.22133040.19358456149100
4.9952-5.38030.21523070.197858116118100
5.3803-5.92060.24493000.219257716071100
5.9206-6.77480.23563000.205357796079100
6.7748-8.52590.21032980.199458496147100
8.5259-44.79890.2533070.19425712601999

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