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- PDB-7fe6: AvmM Catalyzes Macrocyclization in Alchivemycin A Biosynthesis -

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Basic information

Entry
Database: PDB / ID: 7fe6
TitleAvmM Catalyzes Macrocyclization in Alchivemycin A Biosynthesis
ComponentsAvmM
KeywordsBIOSYNTHETIC PROTEIN/INHIBITOR / AvmM / Macrocyclization / Michael addition / BIOSYNTHETIC PROTEIN-INHIBITOR COMPLEX
Function / homologyAlchivemycin A
Function and homology information
Biological speciesStreptomyces sp. NBRC 109436 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925033 China
National Natural Science Foundation of China (NSFC)21861142005 China
CitationJournal: Nat Commun / Year: 2022
Title: AvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis.
Authors: Zhu, H.J. / Zhang, B. / Wei, W. / Liu, S.H. / Xiang, L. / Zhu, J. / Jiao, R.H. / Igarashi, Y. / Bashiri, G. / Liang, Y. / Tan, R.X. / Ge, H.M.
History
DepositionJul 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AvmM
B: AvmM
C: AvmM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,91511
Polymers65,1013
Non-polymers8148
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-68 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.450, 73.450, 242.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and resid 9 through 197)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 9 - 197 / Label seq-ID: 9 - 197

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3(chain C and resid 9 through 197)CC

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Components

#1: Protein AvmM


Mass: 21700.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NBRC 109436 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZHU / Alchivemycin A


Mass: 565.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H51NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate 6.5 and 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→80.8 Å / Num. obs: 24010 / % possible obs: 100 % / Redundancy: 15.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.051 / Rrim(I) all: 0.206 / Net I/σ(I): 11.2 / Num. measured all: 380456 / Scaling rejects: 349
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.616.61.8694409526550.6340.4681.9281.9100
9.01-80.812.50.07478496270.9970.0210.07826.698.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FE0

7fe0


Resolution: 2.5→60.6 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1999 8.36 %
Rwork0.1896 21922 -
obs0.194 23921 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.69 Å2 / Biso mean: 60.1363 Å2 / Biso min: 34.11 Å2
Refinement stepCycle: final / Resolution: 2.5→60.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4431 0 34 66 4531
Biso mean--69.98 51.93 -
Num. residues----567
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2736X-RAY DIFFRACTION13.735TORSIONAL
12B2736X-RAY DIFFRACTION13.735TORSIONAL
13C2736X-RAY DIFFRACTION13.735TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.36641390.320715251664100
2.56-2.630.31761400.27715341674100
2.63-2.710.2841390.258515231662100
2.71-2.80.31021380.251715291667100
2.8-2.90.33161410.250315431684100
2.9-3.010.28421390.239815251664100
3.01-3.150.28691430.22715621705100
3.15-3.320.28681400.200115381678100
3.32-3.520.23581420.199315641706100
3.52-3.80.24251420.186415531695100
3.8-4.180.21251450.152115791724100
4.18-4.780.17251450.131715941739100
4.78-6.020.22211470.150116181765100
6.02-60.60.22351590.19151735189499
Refinement TLS params.Method: refined / Origin x: 30.8063 Å / Origin y: 1.7686 Å / Origin z: 102.7374 Å
111213212223313233
T0.4054 Å20.0231 Å2-0.0801 Å2-0.4626 Å2-0.0995 Å2--0.4185 Å2
L2.1063 °2-0.294 °2-0.4877 °2-2.095 °2-0.1829 °2--1.233 °2
S-0.1684 Å °-0.128 Å °0.0183 Å °0.4018 Å °0.1067 Å °-0.1456 Å °0.2145 Å °0.0784 Å °0.0676 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 197
2X-RAY DIFFRACTION1allB9 - 197
3X-RAY DIFFRACTION1allC9 - 201
4X-RAY DIFFRACTION1allS1 - 67
5X-RAY DIFFRACTION1allE1 - 7

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