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- PDB-7nm7: The crystal structure of the antimycin pathway standalone ketored... -

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Basic information

Entry
Database: PDB / ID: 7nm7
TitleThe crystal structure of the antimycin pathway standalone ketoreductase, AntM
ComponentsAntimycin pathway standalone ketoreductase enzyme, AntM
KeywordsOXIDOREDUCTASE / Ketoreductase / Standalone / Antimycin / Polyketide
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFazal, A. / Hemsworth, G.R. / Webb, M.E. / Seipke, R.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: A Standalone beta-Ketoreductase Acts Concomitantly with Biosynthesis of the Antimycin Scaffold.
Authors: Fazal, A. / Hemsworth, G.R. / Webb, M.E. / Seipke, R.F.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Antimycin pathway standalone ketoreductase enzyme, AntM


Theoretical massNumber of molelcules
Total (without water)30,0251
Polymers30,0251
Non-polymers00
Water95553
1
AAA: Antimycin pathway standalone ketoreductase enzyme, AntM

AAA: Antimycin pathway standalone ketoreductase enzyme, AntM

AAA: Antimycin pathway standalone ketoreductase enzyme, AntM

AAA: Antimycin pathway standalone ketoreductase enzyme, AntM


Theoretical massNumber of molelcules
Total (without water)120,0994
Polymers120,0994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area13330 Å2
ΔGint-92 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.897, 87.897, 116.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Antimycin pathway standalone ketoreductase enzyme, AntM


Mass: 30024.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Strain: S4 / Gene: antM / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citrate phosphate buffer, pH 4.2, 0.2 M NaCl, and 10% w/v PEG 3K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→63.69 Å / Num. obs: 16855 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.997 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 1281 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4osp

4osp


Resolution: 2.1→63.69 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2727 770 4.787 %
Rwork0.2135 15315 -
all0.216 --
obs-16085 99.826 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.008 Å21.004 Å20 Å2
2--2.008 Å20 Å2
3----6.515 Å2
Refinement stepCycle: LAST / Resolution: 2.1→63.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 53 1829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131807
X-RAY DIFFRACTIONr_bond_other_d0.0370.0171694
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6372462
X-RAY DIFFRACTIONr_angle_other_deg2.5161.5723877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22419.76786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02215252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3581517
X-RAY DIFFRACTIONr_chiral_restr0.0650.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022104
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02403
X-RAY DIFFRACTIONr_nbd_refined0.2150.2413
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.21602
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2916
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.2829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.226
X-RAY DIFFRACTIONr_nbd_other0.2280.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5510.212
X-RAY DIFFRACTIONr_mcbond_it3.6674.569985
X-RAY DIFFRACTIONr_mcbond_other3.6514.568984
X-RAY DIFFRACTIONr_mcangle_it4.9016.8321226
X-RAY DIFFRACTIONr_mcangle_other4.96.8331227
X-RAY DIFFRACTIONr_scbond_it4.3364.934821
X-RAY DIFFRACTIONr_scbond_other4.3364.935821
X-RAY DIFFRACTIONr_scangle_it6.1427.2411235
X-RAY DIFFRACTIONr_scangle_other6.1347.2421235
X-RAY DIFFRACTIONr_lrange_it11.71756.052014
X-RAY DIFFRACTIONr_lrange_other11.72356.0552012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.424520.361104X-RAY DIFFRACTION99.3981
2.155-2.2140.339650.331066X-RAY DIFFRACTION100
2.214-2.2780.247450.2921066X-RAY DIFFRACTION100
2.278-2.3480.326550.2691003X-RAY DIFFRACTION99.8113
2.348-2.4250.281470.247999X-RAY DIFFRACTION99.9045
2.425-2.510.309450.224960X-RAY DIFFRACTION99.9006
2.51-2.6050.265370.22936X-RAY DIFFRACTION99.8973
2.605-2.7110.322520.199880X-RAY DIFFRACTION99.8928
2.711-2.8310.266470.192865X-RAY DIFFRACTION100
2.831-2.9690.254520.194813X-RAY DIFFRACTION99.8845
2.969-3.130.259460.201786X-RAY DIFFRACTION99.88
3.13-3.320.259300.229757X-RAY DIFFRACTION99.6203
3.32-3.5490.334360.204708X-RAY DIFFRACTION100
3.549-3.8330.249310.185672X-RAY DIFFRACTION99.858
3.833-4.1980.232320.184603X-RAY DIFFRACTION99.8428
4.198-4.6930.193210.174572X-RAY DIFFRACTION100
4.693-5.4170.273240.168514X-RAY DIFFRACTION100
5.417-6.6310.285240.19437X-RAY DIFFRACTION99.7836
6.631-9.3630.272180.179348X-RAY DIFFRACTION99.7275
9.363-63.690.242110.283226X-RAY DIFFRACTION98.75

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