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- PDB-7sfn: Crystal structure of OlmO, a spirocyclase involved in the biosynt... -

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Basic information

Entry
Database: PDB / ID: 7sfn
TitleCrystal structure of OlmO, a spirocyclase involved in the biosynthesis of oligomycin
ComponentsOlmO - oligomycin spirocyclase
KeywordsHYDROLASE / cyclase / spyrocyclase / oligomycin / calycin
Function / homologyD-MALATE / NlmOI
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBilyk, O. / Leadlay, P.F. / Dias, M.V.B.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)18/00351-1 Brazil
Sao Paulo Research Foundation (FAPESP)20/03850-9 Brazil
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis.
Authors: Bilyk, O. / Oliveira, G.S. / de Angelo, R.M. / Almeida, M.O. / Honorio, K.M. / Leeper, F.J. / Dias, M.V.B. / Leadlay, P.F.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OlmO - oligomycin spirocyclase
B: OlmO - oligomycin spirocyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2553
Polymers43,1212
Non-polymers1341
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-10 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.036, 54.036, 245.493
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein OlmO - oligomycin spirocyclase


Mass: 21560.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: SAV14893_021330, SAV31267_066240
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q93HI7
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3 M Malic acid, pH = 6.0 pH = 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 R 100K-A / Detector: PIXEL / Date: Mar 25, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→49.1 Å / Num. obs: 23608 / % possible obs: 99.6 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.078 / Net I/σ(I): 17.6 / Num. measured all: 221286 / Scaling rejects: 40
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
2.1-2.168.10.7111512718620.8630.2650.76395.1
8.9-49.19.10.03629913300.9990.0120.03845.199.9

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX18.1.3865refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.73 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1088 4.63 %
Rwork0.1706 22412 -
obs0.1722 23500 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.2 Å2 / Biso mean: 50.5205 Å2 / Biso min: 29.13 Å2
Refinement stepCycle: final / Resolution: 2.1→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 9 170 2612
Biso mean--66.54 54.45 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.190.27821180.2212740285898
2.19-2.310.24111280.185928102938100
2.31-2.450.25241440.207628312975100
2.45-2.640.2271500.188627592909100
2.64-2.910.22071290.204828272956100
2.91-3.330.21231490.173227952944100
3.33-4.190.17831430.150128142957100
4.2-43.730.19291270.156628362963100
Refinement TLS params.Method: refined / Origin x: 14.9718 Å / Origin y: 3.3919 Å / Origin z: 133.0074 Å
111213212223313233
T0.3108 Å2-0.0022 Å20.0016 Å2-0.199 Å20.0146 Å2--0.3054 Å2
L0.8821 °20.212 °20.3863 °2-0.9362 °21.1111 °2--3.2949 °2
S0.0436 Å °0.0096 Å °0.0068 Å °-0.0242 Å °-0.1179 Å °0.0214 Å °-0.0083 Å °0.1409 Å °0.0843 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 167
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allB12 - 167
4X-RAY DIFFRACTION1allS1 - 178

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