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- PDB-5es6: Crystal structure of the first two domains of the initiation modu... -

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Basic information

Entry
Database: PDB / ID: 5es6
TitleCrystal structure of the first two domains of the initiation module of LgrA
ComponentsLinear gramicidin synthase subunit A
KeywordsLIGASE / NRPS / initiation module / 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 / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / 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 / molecular replacement / Resolution: 2.46 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7214
Polymers77,5831
Non-polymers1383
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-0 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.320, 161.320, 138.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Linear gramicidin synthase subunit A


Mass: 77583.281 Da / Num. of mol.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 5.79 Å3/Da / Density % sol: 81.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2 M Na-formate, 0.1 M Na-Acetate pH 5.3

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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: Sep 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.46→63.945 Å / Num. obs: 66592 / % possible obs: 100 % / Redundancy: 9.8 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.107 / Rsym value: 0.101 / Net I/av σ(I): 5.258 / Net I/σ(I): 12.5 / Num. measured all: 649606
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.46-2.599.21.2890.68847195940.4441.2891.7100
2.59-2.759.90.7819025590760.2590.782.9100
2.75-2.949.90.4831.68504185560.1610.4834.6100
2.94-3.189.90.25537929179790.0850.2557.8100
3.18-3.489.90.1514.77321573770.050.15112.6100
3.48-3.899.90.0897.56593766550.0290.08918.6100
3.89-4.499.80.0619.95880159720.020.06124.3100
4.49-5.59.80.0717.94935050520.0240.07127.5100
5.5-7.789.60.078.63836539970.0230.0728.1100
7.78-63.9458.90.04411.22088023340.0160.04430.699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
iMOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMU

1amu


Resolution: 2.46→63.954 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 3324 5 %
Rwork0.2225 63182 -
obs0.2239 66506 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 247.96 Å2 / Biso mean: 80.2285 Å2 / Biso min: 39.29 Å2
Refinement stepCycle: final / Resolution: 2.46→63.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 14 66 4724
Biso mean--77.38 75.11 -
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024755
X-RAY DIFFRACTIONf_angle_d0.636446
X-RAY DIFFRACTIONf_chiral_restr0.027711
X-RAY DIFFRACTIONf_plane_restr0.003840
X-RAY DIFFRACTIONf_dihedral_angle_d11.7031757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.46-2.49510.45661350.43382579271499
2.4951-2.53240.46071370.415825862723100
2.5324-2.5720.38741360.387525862722100
2.572-2.61410.41461380.36226292767100
2.6141-2.65920.36611370.346425882725100
2.6592-2.70760.39031360.333625922728100
2.7076-2.75960.36461370.311426042741100
2.7596-2.8160.31221370.313725992736100
2.816-2.87720.3351370.306826112748100
2.8772-2.94410.3741370.304825952732100
2.9441-3.01780.34731360.298426112747100
3.0178-3.09930.35621380.296926092747100
3.0993-3.19050.33591370.286926142751100
3.1905-3.29350.32891380.278326222760100
3.2935-3.41120.2811380.254126172755100
3.4112-3.54780.25571390.252526372776100
3.5478-3.70920.2761370.234926142751100
3.7092-3.90480.23871390.212826402779100
3.9048-4.14940.19331400.179126562796100
4.1494-4.46970.20251390.172726462785100
4.4697-4.91930.18591410.159126682809100
4.9193-5.63080.19081420.164326912833100
5.6308-7.09280.19091430.18227252868100
7.0928-63.97520.20441500.172228633013100

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