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- PDB-8a1a: Structure of a leucinostatin derivative determined by host lattic... -

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Basic information

Entry
Database: PDB / ID: 8a1a
TitleStructure of a leucinostatin derivative determined by host lattice display : L1F11V1 construct
Components
  • 6-(2-methoxyethoxy)-11,15-dimethyl-8-oxa-2,11,15,19,21,23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one
  • L1F11v1
KeywordsDE NOVO PROTEIN / Host lattice display / leucinostatin / EngBF / DARPin
Function / homologyBeta-galactosidase; Chain A, domain 5 - #10 / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Mainly Beta / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsMittl, P.R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structure of a hydrophobic leucinostatin derivative determined by host lattice display.
Authors: Kiss, C. / Gall, F.M. / Dreier, B. / Adams, M. / Riedl, R. / Pluckthun, A. / Mittl, P.R.E.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L1F11v1
B: 6-(2-methoxyethoxy)-11,15-dimethyl-8-oxa-2,11,15,19,21,23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,24015
Polymers148,2102
Non-polymers1,02913
Water27,7071538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-103 kcal/mol
Surface area50100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.866, 191.866, 122.409
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein L1F11v1


Mass: 147035.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: host lattice / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide 6-(2-methoxyethoxy)-11,15-dimethyl-8-oxa-2,11,15,19,21,23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one


Mass: 1174.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 1551 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1538 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.38 Å3/Da
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.43
Details: 3.64 % PEG20000, 24.82 % MPD 0.2M NaCl, 0.01M MnCl2, 0.1M MES, pH 6.43

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→166 Å / Num. obs: 123411 / % possible obs: 96.2 % / Redundancy: 42.4 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.045 / Rrim(I) all: 0.294 / Net I/σ(I): 13.9
Reflection shellResolution: 2.05→2.24 Å / Redundancy: 40.6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6170 / CC1/2: 0.698 / Rpim(I) all: 0.51 / % possible all: 70.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QFK

6qfk


Resolution: 2.05→49.28 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 6165 -RANDOM
Rwork0.1613 ---
obs0.1625 123393 77.2 %-
Displacement parametersBiso mean: 49.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.0554 Å20 Å20 Å2
2---0.0554 Å20 Å2
3---0.1109 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.05→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10343 0 136 1538 12017
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810783HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0114662HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3737SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1898HARMONIC5
X-RAY DIFFRACTIONt_it10770HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1384SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact10540SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion16.77
LS refinement shellResolution: 2.05→2.17 Å
RfactorNum. reflection% reflection
Rfree0.2168 132 -
Rwork0.2343 --
obs0.2334 2468 9.59 %

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