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- PDB-9bou: Crystal structure of ATP-grasp ligase PruB from Streptomyces coel... -

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Basic information

Entry
Database: PDB / ID: 9bou
TitleCrystal structure of ATP-grasp ligase PruB from Streptomyces coelicolor A3(2)
ComponentsMvdD-like pre-ATP grasp domain-containing protein
KeywordsLIGASE / ATP-grasp ligase / peptide cyclase / RiPP biosynthesis
Function / homologyATP-grasp ribosomal peptide maturase, SAV-5884 family / : / MvdD pre-ATP grasp domain / ribosomal S6-glutamic acid ligase activity / SOS response / cytoplasm / MvdD-like pre-ATP grasp domain-containing protein
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsPatel, K.P. / Bruner, S.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128742 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145426 United States
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Characterization of a Dual Function Peptide Cyclase in Graspetide Biosynthesis.
Authors: Rubin, G.M. / Patel, K.P. / Jiang, Y. / Ishee, A.C. / Seabra, G. / Bruner, S.D. / Ding, Y.
History
DepositionMay 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MvdD-like pre-ATP grasp domain-containing protein
B: MvdD-like pre-ATP grasp domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5884
Polymers72,3952
Non-polymers1922
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-56 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.040, 222.040, 87.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein MvdD-like pre-ATP grasp domain-containing protein


Mass: 36197.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: SCO0695, SCF42.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L2K8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.7 Å3/Da / Density % sol: 71.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, and 10% (v/v) 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.91→49.65 Å / Num. obs: 24070 / % possible obs: 99.47 % / Redundancy: 2 % / Biso Wilson estimate: 74.47 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.04394 / Rpim(I) all: 0.04394 / Rrim(I) all: 0.06214 / Net I/σ(I): 8.86
Reflection shellResolution: 2.91→3.014 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3514 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 2331 / CC1/2: 0.683 / CC star: 0.901 / Rpim(I) all: 0.3514 / Rrim(I) all: 0.497 / % possible all: 97.38

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→49.65 Å / SU ML: 0.4383 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6542
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 1201 5 %
Rwork0.2073 22839 -
obs0.2099 24040 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.08 Å2
Refinement stepCycle: LAST / Resolution: 2.91→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 10 26 4427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01344504
X-RAY DIFFRACTIONf_angle_d1.43356135
X-RAY DIFFRACTIONf_chiral_restr0.0617672
X-RAY DIFFRACTIONf_plane_restr0.0201808
X-RAY DIFFRACTIONf_dihedral_angle_d7.2362638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.020.36061180.35022407X-RAY DIFFRACTION96.97
3.02-3.160.38431470.28672479X-RAY DIFFRACTION99.55
3.16-3.330.28411420.24042513X-RAY DIFFRACTION99.74
3.33-3.540.3141220.24292522X-RAY DIFFRACTION99.66
3.54-3.810.30221210.22322537X-RAY DIFFRACTION99.74
3.81-4.190.26181470.18452526X-RAY DIFFRACTION99.89
4.19-4.80.22281230.16922575X-RAY DIFFRACTION99.96
4.8-6.040.24761450.19852567X-RAY DIFFRACTION99.93
6.05-49.650.20221360.18662713X-RAY DIFFRACTION99.75

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