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- PDB-6qep: EngBF DARPin Fusion 4b H14 -

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Basic information

Entry
Database: PDB / ID: 6qep
TitleEngBF DARPin Fusion 4b H14
ComponentsPEGA domain-containing protein,EngBF-DARPin Fusion 4b H14
KeywordsHYDROLASE / crystallization chaperone / protein fusion / DARPin / chaperone
Function / homology
Function and homology information


Designed single chain three-helix bundle / Beta-galactosidase; Chain A, domain 5 - #10 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsErnst, P. / Pluckthun, A. / Mittl, P.R.E.
CitationJournal: Sci Rep / Year: 2019
Title: Structural analysis of biological targets by host:guest crystal lattice engineering.
Authors: Ernst, P. / Pluckthun, A. / Mittl, P.R.E.
History
DepositionJan 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEGA domain-containing protein,EngBF-DARPin Fusion 4b H14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1517
Polymers147,6171
Non-polymers5336
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-22 kcal/mol
Surface area49180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.690, 192.690, 123.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PEGA domain-containing protein,EngBF-DARPin Fusion 4b H14


Mass: 147617.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: DXD52_03130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A374RF80
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: 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
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 4.5 Å3/Da / Density % sol: 72.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6.1
Details: MPD, PEG 20,000, sodium chloride, manganese chloride, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.6→46.28 Å / Num. obs: 80365 / % possible obs: 99.91 % / Redundancy: 20.9 % / Biso Wilson estimate: 81.65 Å2 / Rrim(I) all: 0.172 / Net I/σ(I): 16.78
Reflection shellResolution: 2.6→2.693 Å / Rrim(I) all: 3.263

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 2.6→46.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4017 5 %RANDOM
Rwork0.177 ---
obs0.179 80329 99.9 %-
Displacement parametersBiso mean: 89.26 Å2
Baniso -1Baniso -2Baniso -3
1--4.343 Å20 Å20 Å2
2---4.343 Å20 Å2
3---8.686 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.6→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10299 0 24 573 10896
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110517HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2314265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3619SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1845HARMONIC5
X-RAY DIFFRACTIONt_it10517HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion19.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1362SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12377SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.62 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2702 -4.98 %
Rwork0.2394 1527 -
all0.2411 1607 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 78.3044 Å / Origin y: -29.716 Å / Origin z: 0.0517 Å
111213212223313233
T-0.3014 Å20.0562 Å2-0.0657 Å2--0.4403 Å2-0.0203 Å2---0.3605 Å2
L0.4905 °2-0.2245 °20.0019 °2-1.0848 °2-0.0497 °2--1.1447 °2
S-0.1295 Å °-0.0378 Å °0.1326 Å °0.0341 Å °-0.0527 Å °0.2257 Å °-0.2725 Å °-0.2615 Å °0.1822 Å °
Refinement TLS groupSelection details: { A|* }

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