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- PDB-6ksu: Crystal structure of SurE -

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Basic information

Entry
Database: PDB / ID: 6ksu
TitleCrystal structure of SurE
ComponentsAlpha/beta hydrolaseAlpha/beta hydrolase superfamily
KeywordsHYDROLASE / NRPS / cyclase / PBP-binding protein
Function / homology
Function and homology information


Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
MALONATE ION / YTTRIUM (III) ION / : / Thioesterase
Similarity search - Component
Biological speciesStreptomyces albidoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhai, R. / Mori, T. / Abe, I.
CitationJournal: Nat Catal / Year: 2020
Title: Heterochiral coupling in non-ribosomal peptide macrolactamization
Authors: Matsuda, K. / Zhai, R. / Mori, T. / Kobayashi, M. / Sano, A. / Abe, I. / Wakimoto, T.
History
DepositionAug 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8618
Polymers99,2852
Non-polymers5756
Water5,747319
1
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8413
Polymers49,6431
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19030 Å2
MethodPISA
2
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0205
Polymers49,6431
Non-polymers3774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.738, 150.370, 64.771
Angle α, β, γ (deg.)90.000, 110.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha/beta hydrolase / Alpha/beta hydrolase superfamily / SurE


Mass: 49642.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albidoflavus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Q6RSJ1, UniProt: A0A679G4U8*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: ammonium sulfate, Ytterium, TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.18 Å / Num. obs: 44668 / % possible obs: 99.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 27.61 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3901 / CC1/2: 0.607

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: selenomethionine-labeled SurE

Resolution: 2.2→46.525 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.69
RfactorNum. reflection% reflection
Rfree0.2579 2009 4.5 %
Rwork0.2119 --
obs0.214 44606 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.27 Å2 / Biso mean: 34.1527 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 2.2→46.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6539 0 28 319 6886
Biso mean--55.49 34.44 -
Num. residues----881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.33571390.27663083100
2.255-2.3160.33591530.26253026100
2.316-2.38410.29441390.26593079100
2.3841-2.46110.29311390.25113040100
2.4611-2.54910.29851470.24123058100
2.5491-2.65110.33591490.23953066100
2.6511-2.77170.28681400.2323304599
2.7717-2.91790.2911420.2359303099
2.9179-3.10060.29651430.2244306499
3.1006-3.340.28031470.2117302999
3.34-3.6760.24521430.1955302299
3.676-4.20760.21681420.1832302798
4.2076-5.29990.18581500.1683302298
5.2999-46.5250.23151360.1971300696

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