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- PDB-6ksv: Crystal structure of SurE with D-Leu -

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Basic information

Entry
Database: PDB / ID: 6ksv
TitleCrystal structure of SurE with D-Leu
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
D-LEUCINE / Chem-E7L / YTTRIUM (III) ION / : / Thioesterase
Similarity search - Component
Biological speciesStreptomyces albidoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)100,39612
Polymers99,2852
Non-polymers1,11110
Water1,946108
1
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2407
Polymers49,6431
Non-polymers5976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area17720 Å2
MethodPISA
2
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1565
Polymers49,6431
Non-polymers5134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.370, 152.060, 64.540
Angle α, β, γ (deg.)90.000, 113.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Q6RSJ1, UniProt: A0A679G4U8*PLUS

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Non-polymers , 5 types, 118 molecules

#2: Chemical ChemComp-DLE / D-LEUCINE / Leucine


Type: D-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Y
#5: Chemical ChemComp-E7L / S-(2-acetamidoethyl) (2R)-2-azanyl-4-methyl-pentanethioate


Mass: 232.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20N2O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: ammonium sulfate, Yttrium Chloride, TCEP

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Data collection

DiffractionMean temperature: 277 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: Feb 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4197→50 Å / Num. obs: 32476 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 44.23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.41
Reflection shellResolution: 2.4197→2.57 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 5134 / CC1/2: 0.839 / % possible all: 97.7

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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: 6KSU

6ksu


Resolution: 2.42→45.086 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.23
RfactorNum. reflection% reflection
Rfree0.2788 1622 5 %
Rwork0.2001 --
obs0.2039 32449 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.27 Å2 / Biso mean: 43.9924 Å2 / Biso min: 17.47 Å2
Refinement stepCycle: final / Resolution: 2.42→45.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 51 108 6489
Biso mean--59.37 40.4 -
Num. residues----853
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.42-2.49090.35721290.2813246796
2.4909-2.57130.3431360.2653257699
2.5713-2.66320.32481350.25782564100
2.6632-2.76980.31681350.23512563100
2.7698-2.89590.31871360.22992585100
2.8959-3.04850.3491360.22172577100
3.0485-3.23940.26831360.2232583100
3.2394-3.48950.27621330.19852539100
3.4895-3.84050.27251350.179257699
3.8405-4.39580.24741360.1692588100
4.3958-5.53660.24581360.17632584100
5.5366-45.0860.26451390.19222625100

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