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- PDB-6qev: EngBF DARPin Fusion 4b B6 -

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Basic information

Entry
Database: PDB / ID: 6qev
TitleEngBF DARPin Fusion 4b B6
Components
  • PEGA domain-containing protein,PEGA domain-containing protein,EngBF DARPin fusion B6 complex
  • PRO-LYS-SER-ILE-ARG-ILE-GLY-PRO-GLY-GLN-ALA-PHE-TYR-ALA-DPR
KeywordsHYDROLASE / crystallization chaperone / protein fusion / DARPin / CHAPERONE
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase activity / carbohydrate binding / membrane => GO:0016020
Similarity search - Function
Glycosyl hydrolase 101, beta-sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Glycosyl hydrolase 101 beta sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase N-terminal domain / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase ...Glycosyl hydrolase 101, beta-sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Glycosyl hydrolase 101 beta sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase N-terminal domain / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Carboxypeptidase-like, regulatory domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / PEGA domain-containing protein
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: PEGA domain-containing protein,PEGA domain-containing protein,EngBF DARPin fusion B6 complex
D: PRO-LYS-SER-ILE-ARG-ILE-GLY-PRO-GLY-GLN-ALA-PHE-TYR-ALA-DPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0249
Polymers149,4492
Non-polymers5747
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-52 kcal/mol
Surface area49120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.770, 194.770, 123.710
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,PEGA domain-containing protein,EngBF DARPin fusion B6 complex


Mass: 147845.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: DW792_04840 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A414FD23
#2: Protein/peptide PRO-LYS-SER-ILE-ARG-ILE-GLY-PRO-GLY-GLN-ALA-PHE-TYR-ALA-DPR


Mass: 1603.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 4.53 Å3/Da / Density % sol: 72.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6
Details: MPD, sodium chloride, manganese chloride, PEG 20,000, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.7→48.69 Å / Num. obs: 73165 / % possible obs: 99.82 % / Redundancy: 17.6 % / Biso Wilson estimate: 91.69 Å2 / Rrim(I) all: 0.3377 / Net I/σ(I): 8.59
Reflection shellResolution: 2.7→2.797 Å / Rrim(I) all: 3.03

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 2.7→48.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3658 5 %RANDOM
Rwork0.176 ---
obs0.178 73155 99.9 %-
Displacement parametersBiso mean: 71.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.4749 Å20 Å20 Å2
2--2.4749 Å20 Å2
3----4.9497 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.7→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10434 0 35 499 10968
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110668HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2614475HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3655SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1866HARMONIC5
X-RAY DIFFRACTIONt_it10668HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion20.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1382SEMIHARMONIC5
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_contact11960SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.72 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3349 -4.99 %
Rwork0.2748 1391 -
all0.278 1464 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0717-0.1067-0.03560.5466-0.0260.31570.01410.05790.04180.03350.00570.0984-0.1099-0.058-0.0198-0.1293-0.02120.0243-0.18720.0305-0.186481.4974-31.97963.7324
2-1.35870.78450.01331.3587-0.80750-0.0291-0.0849-0.01530.09350.0141-0.065-0.01560.08720.0150.10660.07720.0614-0.04980.0363-0.137174.2454-6.967140.0422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|* }
2X-RAY DIFFRACTION2{ D|* }

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