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- PDB-6sh9: EngBF DARPin Fusion 4b D12 -

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Basic information

Entry
Database: PDB / ID: 6sh9
TitleEngBF DARPin Fusion 4b D12
Components
  • Endo-alpha-N-acetylgalactosaminidase,DARPin 4b D12
  • Envelope glycoprotein gp160
KeywordsHYDROLASE / crystallization chaperone / protein fusion / DARPin / chaperone
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase / endo-alpha-N-acetylgalactosaminidase activity / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane ...endo-alpha-N-acetylgalactosaminidase / endo-alpha-N-acetylgalactosaminidase activity / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
: / Endo-alpha-N-acetylgalactosaminidase, helical bundle domain / : / Endo-alpha-N-acetylgalactosaminidase, domain 5 / 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 ...: / Endo-alpha-N-acetylgalactosaminidase, helical bundle domain / : / Endo-alpha-N-acetylgalactosaminidase, domain 5 / 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 regulatory-like domain / FIVAR domain / 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 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Envelope glycoprotein gp160 / Endo-alpha-N-acetylgalactosaminidase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum JCM 1217 (bacteria)
synthetic construct (others)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionAug 6, 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
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Endo-alpha-N-acetylgalactosaminidase,DARPin 4b D12
E: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0658
Polymers149,5322
Non-polymers5336
Water16,592921
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-41 kcal/mol
Surface area49590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.010, 192.010, 122.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BE

#1: Protein Endo-alpha-N-acetylgalactosaminidase,DARPin 4b D12


Mass: 147910.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum JCM 1217 (bacteria), (gene. exp.) synthetic construct (others)
Gene: engBF / Production host: Escherichia coli (E. coli)
References: UniProt: Q3T552, endo-alpha-N-acetylgalactosaminidase
#2: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 1620.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P05877

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Non-polymers , 4 types, 927 molecules

#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: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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

CrystalDensity Matthews: 4.34 Å3/Da
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: PEG 20,000 MPD 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: 1.0000305674359 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000305674359 Å / Relative weight: 1
ReflectionResolution: 2→49.2 Å / Num. obs: 172028 / % possible obs: 99.9 % / Redundancy: 10.468 % / Biso Wilson estimate: 68.31 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.371 / Rrim(I) all: 0.39 / Χ2: 0.904 / Net I/σ(I): 5.03 / Num. measured all: 1800744 / Scaling rejects: 386
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
2-2.059.55214.170.12120584126721262414.9799.6
2.05-2.1110.65910.3170.21132030123931238710.833100
2.11-2.1710.8467.3140.3213032212022120167.675100
2.17-2.2410.8385.7670.4412640111664116636.0521000.117
2.24-2.3110.6974.6610.5612141211357113504.89599.90.163
2.31-2.3910.5883.2930.7911621610976109763.461000.216
2.39-2.4810.3332.6940.9810890310542105392.8341000.286
2.48-2.589.4662.131.279667810216102132.2541000.336
2.58-2.710.7061.671.82104425975597541.7541000.499
2.7-2.8310.8171.3262.56101340936993691.3921000.647
2.83-2.9810.6110.9393.8494140887388720.9871000.814
2.98-3.1610.6840.6196.0590020842684260.651000.941
3.16-3.3810.5490.3988.3583557792179210.4181000.974
3.38-3.6510.040.23911.3973974736873680.2521000.987
3.65-410.0590.16114.468391679967990.171000.992
4-4.4711.1390.12118.3268480614861480.1261000.995
4.47-5.1610.8970.10620.1759227543554350.1111000.996
5.16-6.3210.4930.11118.9648342460746070.1161000.995
6.32-8.949.7680.08321.1334832356835660.08899.90.997
8.94-49.210.7620.0627.0721470200919950.06399.30.998

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZXQ

2zxq


Resolution: 2.4→49.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4991 5 %RANDOM
Rwork0.161 ---
obs0.163 99813 100 %-
Displacement parametersBiso max: 190.45 Å2 / Biso mean: 60.97 Å2 / Biso min: 29.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.1699 Å20 Å20 Å2
2--1.1699 Å20 Å2
3----2.3399 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.4→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10357 0 24 921 11302
Biso mean--81.4 60.06 -
Num. residues----1349
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3663SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1871HARMONIC5
X-RAY DIFFRACTIONt_it10642HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1378SEMIHARMONIC5
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_contact12581SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10642HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg14446HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion18.79
LS refinement shellResolution: 2.4→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2694 100 5.01 %
Rwork0.2438 1897 -
all0.245 1997 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 80.5084 Å / Origin y: -31.3872 Å / Origin z: 3.9046 Å
111213212223313233
T0.0859 Å2-0.0003 Å20.0412 Å2-0.1273 Å20.0245 Å2--0.1401 Å2
L0.1142 °2-0.1554 °2-0.0214 °2-0.7868 °2-0.0355 °2--0.4115 °2
S0.0059 Å °0.0355 Å °0.0175 Å °0.0357 Å °-0.0121 Å °0.1185 Å °-0.0588 Å °-0.0661 Å °0.0062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A342 - 346
2X-RAY DIFFRACTION1{ *|* }B342 - 346
3X-RAY DIFFRACTION1{ *|* }B342 - 346
4X-RAY DIFFRACTION1{ *|* }C342 - 346
5X-RAY DIFFRACTION1{ *|* }E342 - 346
6X-RAY DIFFRACTION1{ *|* }S342 - 346

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