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- PDB-6qfk: EngBF DARPin Fusion 4b G10 -

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Basic information

Entry
Database: PDB / ID: 6qfk
TitleEngBF DARPin Fusion 4b G10
Components
  • PEGA domain-containing protein,PEGA domain-containing protein,EngBF DARPin fusion G10
  • V3-IF
KeywordsHYDROLASE / crystallization chaperone / protein fusion / DARPin / chaperone
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase activity / membrane => GO:0016020 / carbohydrate binding
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 / Beta-galactosidase; Chain A, domain 5 - #10 / 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 / Beta-galactosidase; Chain A, domain 5 / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / PEGA domain-containing protein
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 10, 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 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEGA domain-containing protein,PEGA domain-containing protein,EngBF DARPin fusion G10
B: V3-IF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,02320
Polymers149,6122
Non-polymers1,41118
Water29,5091638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-18 kcal/mol
Surface area50310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.893, 192.893, 122.922
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 PEGA domain-containing protein,PEGA domain-containing protein,EngBF DARPin fusion G10


Mass: 148007.688 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 V3-IF


Mass: 1603.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 1656 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.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1638 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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

Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6.6
Details: MPD, PEG 20,000, MES, sodium chloride, manganese chloride

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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: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.33 Å / Num. obs: 174930 / % possible obs: 99.98 % / Redundancy: 20.9 % / Biso Wilson estimate: 39.31 Å2 / Rrim(I) all: 0.2538 / Net I/σ(I): 13.46
Reflection shellResolution: 2→2.072 Å / Rrim(I) all: 2.903

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZXQ

2zxq


Resolution: 2→29.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.176 8744 5 %RANDOM
Rwork0.154 ---
obs0.155 174877 100 %-
Displacement parametersBiso mean: 46.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.9285 Å20 Å20 Å2
2--0.9285 Å20 Å2
3----1.857 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 2→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10449 0 87 1638 12174
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110805HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114650HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3724SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1894HARMONIC5
X-RAY DIFFRACTIONt_it10805HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion17.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1388SEMIHARMONIC5
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_contact13649SEMIHARMONIC4
LS refinement shellResolution: 2→2.01 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2756 175 5 %
Rwork0.2359 3323 -
all0.2378 3498 -
obs--99.97 %
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)
10.0774-0.0787-0.00070.3994-0.02280.27960.02960.01320.02790.0083-0.01590.0696-0.0632-0.0281-0.0137-0.0619-0.00930.0201-0.06470.0132-0.038880.6319-31.68653.7414
2-0.22880.098-0.71270.34690.64750.61820.0118-0.0596-0.00720.03350.0118-0.0463-0.02730.025-0.02360.30610.12570.0508-0.1380.2048-0.129873.4325-8.171240.45
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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