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- PDB-7m4s: Crystal structure of macrocyclase AMdnB from Anabaena sp. PCC 7120 -

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Basic information

Entry
Database: PDB / ID: 7m4s
TitleCrystal structure of macrocyclase AMdnB from Anabaena sp. PCC 7120
ComponentsAMdnB protein
KeywordsBIOSYNTHETIC PROTEIN / Natural products / RiPPs / macrocyclase
Function / homology
Function and homology information


ribosomal S6-glutamic acid ligase activity / glutathione synthase activity / SOS response / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
ATP-grasp ribosomal peptide maturase, MvdC family / : / MvdD pre-ATP grasp domain / Prokaryotic glutathione synthetase, ATP-binding / Prokaryotic glutathione synthetase, ATP-grasp domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsLi, G. / Bruner, S.D.
CitationJournal: Proteins / Year: 2022
Title: Structural and biochemical studies of an iterative ribosomal peptide macrocyclase.
Authors: Li, G. / Patel, K. / Zhang, Y. / Pugmire, J.K. / Ding, Y. / Bruner, S.D.
History
DepositionMar 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMdnB protein
B: AMdnB protein
C: AMdnB protein
D: AMdnB protein


Theoretical massNumber of molelcules
Total (without water)165,1424
Polymers165,1424
Non-polymers00
Water84747
1
A: AMdnB protein
D: AMdnB protein


Theoretical massNumber of molelcules
Total (without water)82,5712
Polymers82,5712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-32 kcal/mol
Surface area28110 Å2
MethodPISA
2
B: AMdnB protein
C: AMdnB protein


Theoretical massNumber of molelcules
Total (without water)82,5712
Polymers82,5712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-28 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.479, 132.464, 83.010
Angle α, β, γ (deg.)90.000, 91.005, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

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
11LEULEUSERSER(chain 'A' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))AA3 - 17737 - 211
12LEULEUALAALA(chain 'A' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))AA197 - 236231 - 270
13GLUGLUGLNGLN(chain 'A' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))AA252 - 325286 - 359
21LEULEUSERSER(chain 'B' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))BB3 - 17737 - 211
22LEULEUALAALA(chain 'B' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))BB197 - 236231 - 270
23GLUGLUGLNGLN(chain 'B' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))BB252 - 325286 - 359
31LEULEUSERSER(chain 'C' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))CC3 - 17737 - 211
32LEULEUALAALA(chain 'C' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))CC197 - 236231 - 270
33GLUGLUGLNGLN(chain 'C' and (resid 3 through 178 or resid 197 through 237 or resid 252 through 326))CC252 - 325286 - 359
41LEULEUSERSERchain 'D'DD3 - 17737 - 211
42LEULEUALAALAchain 'D'DD197 - 236231 - 270
43GLUGLUGLNGLNchain 'D'DD252 - 325286 - 359

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Components

#1: Protein
AMdnB protein


Mass: 41285.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YLC3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.05 Å3/Da / Density % sol: 39.9 % / Description: Hexagon-shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5
Details: 0.18 M Tri-ammonium citrate, 20% (w/v) PEG 3350 and 0.012 M praseodymium (III) acetate hydrate
PH range: 8.5 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.493→41.5 Å / Num. obs: 45272 / % possible obs: 97.68 % / Redundancy: 6.77 % / Biso Wilson estimate: 44.38 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1459 / Rpim(I) all: 0.06129 / Rrim(I) all: 0.1586 / Net I/σ(I): 9.29
Reflection shellResolution: 2.493→2.582 Å / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 4314 / CC1/2: 0.596 / Rpim(I) all: 0.5103 / % possible all: 93.23

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIXv1.19.2refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ig8

5ig8


Resolution: 2.493→41.5 Å / SU ML: 0.3677 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2576 2339 5.17 %
Rwork0.1986 42902 -
obs0.2016 45241 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.45 Å2
Refinement stepCycle: LAST / Resolution: 2.493→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9891 0 0 47 9938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011910135
X-RAY DIFFRACTIONf_angle_d1.723413781
X-RAY DIFFRACTIONf_chiral_restr0.07581514
X-RAY DIFFRACTIONf_plane_restr0.01091786
X-RAY DIFFRACTIONf_dihedral_angle_d21.75311311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.540.35571470.27452284X-RAY DIFFRACTION89.54
2.54-2.60.31131570.25692492X-RAY DIFFRACTION97.79
2.6-2.660.34511460.25092537X-RAY DIFFRACTION97.74
2.66-2.730.32221550.24052435X-RAY DIFFRACTION98.07
2.73-2.80.37451380.24662547X-RAY DIFFRACTION97.35
2.8-2.880.37171360.24172528X-RAY DIFFRACTION98.48
2.88-2.970.32221410.23772518X-RAY DIFFRACTION97.87
2.98-3.080.30421260.23772556X-RAY DIFFRACTION98.1
3.08-3.20.29551330.21962535X-RAY DIFFRACTION98.49
3.2-3.350.25981290.21462538X-RAY DIFFRACTION98.34
3.35-3.530.28241370.21152552X-RAY DIFFRACTION98.39
3.53-3.750.25971210.19182561X-RAY DIFFRACTION98.68
3.75-4.040.22391410.18182549X-RAY DIFFRACTION98.39
4.04-4.440.22831570.16842537X-RAY DIFFRACTION98.5
4.44-5.080.20421360.162552X-RAY DIFFRACTION98.43
5.08-6.40.21411250.19362578X-RAY DIFFRACTION98.33
6.4-41.50.20311140.17082603X-RAY DIFFRACTION97.7

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