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- PDB-5isx: Structure of the holo PCP-E didomain of the gramicidin S synthetase A -

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Basic information

Entry
Database: PDB / ID: 5isx
TitleStructure of the holo PCP-E didomain of the gramicidin S synthetase A
ComponentsGramicidin S synthase 1
KeywordsISOMERASE / Epimerization domain / NRPS / gramicidin S
Function / homology
Function and homology information


phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / ligase activity / antibiotic biosynthetic process / ATP binding
Similarity search - Function
Non-ribosomal peptide synthase / 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 ...Non-ribosomal peptide synthase / 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 / 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
4'-PHOSPHOPANTETHEINE / Gramicidin S synthase 1
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.335 Å
AuthorsChen, W.-H. / Li, K. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1411991 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Interdomain and Intermodule Organization in Epimerization Domain Containing Nonribosomal Peptide Synthetases.
Authors: Chen, W.H. / Li, K. / Guntaka, N.S. / Bruner, S.D.
History
DepositionMar 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gramicidin S synthase 1
B: Gramicidin S synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2865
Polymers134,4772
Non-polymers8093
Water7,746430
1
A: Gramicidin S synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6893
Polymers67,2391
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gramicidin S synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5972
Polymers67,2391
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.812, 58.039, 90.857
Angle α, β, γ (deg.)90.00, 100.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gramicidin S synthase 1 / Gramicidin S synthase I


Mass: 67238.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: grsA, grs1 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C062, phenylalanine racemase (ATP-hydrolysing)
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 18% PEG 3350, 5% glycerol, and 100 mM sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.335→38.971 Å / % possible obs: 99.3 % / Redundancy: 7.7 % / Net I/σ(I): 3.38

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSOSX10.9.5_Darwin13.4.0data reduction
SCALA3.3.22data scaling
PHASER2.5.6phasing
RefinementResolution: 2.335→38.971 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 1998 4.08 %
Rwork0.1866 --
obs0.1882 48983 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.335→38.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8750 0 50 430 9230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058997
X-RAY DIFFRACTIONf_angle_d0.74712169
X-RAY DIFFRACTIONf_dihedral_angle_d12.7483344
X-RAY DIFFRACTIONf_chiral_restr0.0291318
X-RAY DIFFRACTIONf_plane_restr0.0031560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3351-2.39350.31221330.23943113X-RAY DIFFRACTION92
2.3935-2.45820.27661430.2413361X-RAY DIFFRACTION100
2.4582-2.53050.31661410.22473331X-RAY DIFFRACTION100
2.5305-2.61220.29971420.21563346X-RAY DIFFRACTION100
2.6122-2.70550.28911420.22773320X-RAY DIFFRACTION99
2.7055-2.81380.26891420.2093349X-RAY DIFFRACTION100
2.8138-2.94180.28741430.19953371X-RAY DIFFRACTION100
2.9418-3.09690.24561440.19983370X-RAY DIFFRACTION100
3.0969-3.29080.23071430.19433371X-RAY DIFFRACTION100
3.2908-3.54470.24561410.18713341X-RAY DIFFRACTION99
3.5447-3.90120.18491450.16793385X-RAY DIFFRACTION99
3.9012-4.4650.16981440.15913414X-RAY DIFFRACTION100
4.465-5.62270.18231460.16113402X-RAY DIFFRACTION100
5.6227-38.97680.18891490.16793511X-RAY DIFFRACTION100

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