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- PDB-5ig8: Crystal structure of macrocyclase MdnB from Microcystis aeruginosa MRC -

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Basic information

Entry
Database: PDB / ID: 5ig8
TitleCrystal structure of macrocyclase MdnB from Microcystis aeruginosa MRC
ComponentsATP grasp ligase
KeywordsLIGASE / RiPP / Macrocyclase
Function / homologyATP-grasp ribosomal peptide maturase, MvdC family / : / MvdD pre-ATP grasp domain / ribosomal S6-glutamic acid ligase activity / SOS response / cytoplasm / ATP grasp ligase
Function and homology information
Biological speciesMicrocystis aeruginosa MRC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.278 Å
AuthorsLi, K. / Condurso, H.L. / Bruner, S.D.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural basis for precursor protein-directed ribosomal peptide macrocyclization.
Authors: Li, K. / Condurso, H.L. / Li, G. / Ding, Y. / Bruner, S.D.
History
DepositionFeb 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP grasp ligase
B: ATP grasp ligase


Theoretical massNumber of molelcules
Total (without water)76,0542
Polymers76,0542
Non-polymers00
Water1,02757
1
A: ATP grasp ligase

A: ATP grasp ligase


Theoretical massNumber of molelcules
Total (without water)76,0542
Polymers76,0542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4760 Å2
ΔGint-26 kcal/mol
Surface area28250 Å2
MethodPISA
2
B: ATP grasp ligase

B: ATP grasp ligase


Theoretical massNumber of molelcules
Total (without water)76,0542
Polymers76,0542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3170 Å2
ΔGint-9 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.623, 37.990, 139.385
Angle α, β, γ (deg.)90.00, 116.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ATP grasp ligase


Mass: 38026.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa MRC (bacteria) / Gene: mdnB / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2G3C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4,000, 20% 2-propanol and 100 mM sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.278→36.027 Å / Num. obs: 28107 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 43.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05297 / Net I/σ(I): 17.03
Reflection shellResolution: 2.278→2.359 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4125 / Mean I/σ(I) obs: 3.56 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.278→36.027 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.69
RfactorNum. reflection% reflection
Rfree0.2554 1363 4.85 %
Rwork0.2141 --
obs0.2161 28082 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.278→36.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 0 57 4425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094477
X-RAY DIFFRACTIONf_angle_d0.9916075
X-RAY DIFFRACTIONf_dihedral_angle_d17.912659
X-RAY DIFFRACTIONf_chiral_restr0.058683
X-RAY DIFFRACTIONf_plane_restr0.007788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2779-2.35930.33931310.26382582X-RAY DIFFRACTION97
2.3593-2.45380.31911650.24512608X-RAY DIFFRACTION100
2.4538-2.56540.3211500.2362634X-RAY DIFFRACTION100
2.5654-2.70070.26461280.22322677X-RAY DIFFRACTION100
2.7007-2.86980.25071130.22182673X-RAY DIFFRACTION100
2.8698-3.09130.29891270.23742663X-RAY DIFFRACTION100
3.0913-3.40210.28281410.22262695X-RAY DIFFRACTION100
3.4021-3.89390.26621160.2052697X-RAY DIFFRACTION100
3.8939-4.9040.2111670.18592677X-RAY DIFFRACTION100
4.904-36.03180.23291250.21492813X-RAY DIFFRACTION99

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